Diff of the two buildlogs: -- --- b1/build.log 2024-01-06 20:17:30.929369687 +0000 +++ b2/build.log 2024-01-06 20:41:04.907048794 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 6 07:44:09 -12 2024 -I: pbuilder-time-stamp: 1704570249 +I: Current time: Sat Feb 8 16:40:38 +14 2025 +I: pbuilder-time-stamp: 1738982438 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./rdkit_202009.4-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.KYj1SaYg/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.UnrE4AHc/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 21 10:42:16 2021 gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 gpgv: Can't check signature: No public key @@ -36,49 +36,80 @@ dpkg-source: info: applying sphinx_compile_fixes.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/844879/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/514051/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 8 02:40 /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/514051/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/514051/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='28122b47d9504bfb82667cca16eef5a1' - 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='844879' - PS1='# ' - PS2='> ' + INVOCATION_ID=93a14c067a8543f8a651168d20792c2f + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=514051 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.WOYyHNDW/pbuilderrc_pRGI --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WOYyHNDW/b1 --logfile b1/build.log rdkit_202009.4-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.WOYyHNDW/pbuilderrc_noX6 --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WOYyHNDW/b2 --logfile b2/build.log rdkit_202009.4-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash @@ -138,7 +169,7 @@ -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 7 09:30 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 8 02:40 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su @@ -164,7 +195,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/844879/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/514051/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -559,7 +590,7 @@ Get: 288 http://deb.debian.org/debian bullseye/main amd64 texlive-latex-recommended all 2020.20210202-3 [14.5 MB] Get: 289 http://deb.debian.org/debian bullseye/main amd64 texlive-pictures all 2020.20210202-3 [6743 kB] Get: 290 http://deb.debian.org/debian bullseye/main amd64 texlive-latex-extra all 2020.20210202-3 [13.7 MB] -Fetched 314 MB in 30s (10.6 MB/s) +Fetched 314 MB in 3s (99.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17743 files and directories currently installed.) @@ -1489,8 +1520,8 @@ Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jan 6 19:45:41 UTC 2024. -Universal Time is now: Sat Jan 6 19:45:41 UTC 2024. +Local time is now: Sat Feb 8 02:41:39 UTC 2025. +Universal Time is now: Sat Feb 8 02:41:39 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1+nmu1) ... @@ -1825,7 +1856,11 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/rdkit-202009.4/ && 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_202009.4-1_source.changes +I: user script /srv/workspace/pbuilder/514051/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/514051/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202009.4/ && 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_202009.4-1_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202009.4-1 dpkg-buildpackage: info: source distribution unstable @@ -2093,7 +2128,7 @@ make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' dh_auto_build dh_auto_build: warning: Compatibility levels before 10 are deprecated (level 9 in use) - cd obj-x86_64-linux-gnu && make -j15 VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202009.4 -B/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2111,86 +2146,86 @@ cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/RingFamilies /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch/CMakeFiles/catch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch/CMakeFiles/catch.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch/CMakeFiles/catch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/depend.internal". +Scanning dependencies of target coordgen_support Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend.internal". 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/depend.internal". +Scanning dependencies of target RDStreams Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend.internal". -Scanning dependencies of target RDStreams -Scanning dependencies of target hc -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build +Scanning dependencies of target hc +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build Scanning dependencies of target RDGeneral -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 0%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o +[ 0%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd 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/build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh/hcdriver.c cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDStreams/streams.cpp -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDLog.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh/hc.c +[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o +[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/utils.cpp +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Invariant.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh/hc.c cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/types.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/Invariant.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/RDLog.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/versions.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/utils.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/LocaleSwitcher.cpp [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 @@ -2213,24 +2248,24 @@ make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDBoost /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake --color= +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend -make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend @@ -2238,150 +2273,164 @@ cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Catalogs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Query /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend.internal". make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/depend.internal". Scanning dependencies of target testConcurrentQueue Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/depend.internal". Scanning dependencies of target RDBoost +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend.internal". Scanning dependencies of target EigenSolvers -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/depend.internal". Scanning dependencies of target testDict +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/depend.internal". +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build +Scanning dependencies of target testMatCalc +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Scanning dependencies of target testQuery -Scanning dependencies of target testMatrices -Scanning dependencies of target testRDValue make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Scanning dependencies of target Catalogs make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build +Scanning dependencies of target testRDValue make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build +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-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build +Scanning dependencies of target testMatrices make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build +Scanning dependencies of target Catalogs make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target SimDivPickers make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend.internal". -Scanning dependencies of target testMatCalc -Scanning dependencies of target DataStructs +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -[ 1%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 1%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target DataStructs +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build +[ 1%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o +[ 1%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o +[ 1%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -[ 1%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend.internal". -[ 1%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Query/test.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/testMatrices.cpp +[ 1%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/testDict.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/testConcurrentQueue.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Catalogs/Catalog.cpp -Scanning dependencies of target SimDivPickers -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 1%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Query/test.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDGeneral/testRDValue.cpp -[ 1%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o +[ 1%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o +[ 1%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.cpp -[ 1%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Catalogs/CatalogEntry.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/ExplicitBitVect.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202009.4/Code/Catalogs/CatalogEntry.cpp +[ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/ExplicitBitVect.cpp +[ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 5%] Built target SimDivPickers +make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend.internal". +Scanning dependencies of target testSimDivPickers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/testPickers.cpp +[ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2020.09.4 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 5%] Built target Catalogs +[ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 5%] Built target EigenSolvers In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2403,20 +2452,11 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 5%] Built target SimDivPickers -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend.internal". -Scanning dependencies of target testSimDivPickers +[ 5%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/testPickers.cpp +[ 5%] Built target testMatrices [ 5%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2020.09.4 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so @@ -2424,32 +2464,27 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 5%] Built target RDBoost make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= -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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend.internal". Scanning dependencies of target rdBase make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend.internal". Scanning dependencies of target Clustering make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build -[ 5%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 5%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp [ 5%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh/Clustering.cpp -[ 5%] Linking CXX executable testMatrices -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 5%] Built target testMatrices [ 5%] Linking CXX executable testQuery cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl @@ -2460,154 +2495,138 @@ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 5%] Built target testSimDivPickers -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2020.09.4 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -In file included from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp:14: -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 285 | if (df_isTextMode && c > STD_ASCII) { - | ~~^~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 297 | if ((!df_isTextMode || c <= STD_ASCII) && - | ~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 308 | if (df_isTextMode && c > STD_ASCII && - | ~~^~~~~~~~~~~ cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 5%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend.internal". Scanning dependencies of target testMultiFPB Scanning dependencies of target testFPB Scanning dependencies of target testDataStructs make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build -Scanning dependencies of target RDGeometryLib -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend.internal". -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend.internal". -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend.internal". -Scanning dependencies of target InfoTheory make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend.internal". +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +Scanning dependencies of target RDGeometryLib make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend.internal". -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -Scanning dependencies of target rdMetricMatrixCalc make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build +Scanning dependencies of target pickersTestsCatch +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend.internal". make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/testMultiFPB.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target InfoTheory make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build -Scanning dependencies of target pickersTestsCatch -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/testFPB.cpp -Scanning dependencies of target cDataStructs -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build +Scanning dependencies of target rdMetricMatrixCalc make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build -Scanning dependencies of target rdSimDivPickers -[ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o [ 5%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/testFPB.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/testDatastructs.cpp +Scanning dependencies of target rdSimDivPickers +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/testMultiFPB.cpp +[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform2D.cpp -[ 5%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o +[ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build +[ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o +[ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o +[ 5%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/catch_tests.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/InfoBitRanker.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o +Scanning dependencies of target cDataStructs cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform2D.cpp +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform3D.cpp [ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/catch_tests.cpp -[ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Transform3D.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 5%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o +cd 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/build/reproducible-path/rdkit-202009.4/Code/Geometry/UniformGrid3D.cpp +[ 5%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/DataStructs.cpp -[ 6%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/MaxMinPicker.cpp -[ 7%] Linking CXX executable testRDValue -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/UniformGrid3D.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2629,36 +2648,40 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 7%] Linking CXX executable testRDValue +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +In file included from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap/RDBase.cpp:14: +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 285 | if (df_isTextMode && c > STD_ASCII) { + | ~~^~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 297 | if ((!df_isTextMode || c <= STD_ASCII) && + | ~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 308 | if (df_isTextMode && c > STD_ASCII && + | ~~^~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 7%] Built target testRDValue +[ 7%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 7%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o 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-I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/DiscreteValueVect.cpp +[ 7%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/SparseIntVect.cpp [ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/GridUtils.cpp -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/SparseIntVect.cpp -[ 8%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_SparseBV.cpp +[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp +[ 8%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Built target InfoTheory -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend.internal". -Scanning dependencies of target rdInfoTheory -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2673,7 +2696,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/DataStructs.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2694,18 +2717,17 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/DataStructs.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp -[ 8%] Linking CXX executable testDict -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 8%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/LeaderPicker.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2724,9 +2746,24 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 8%] Built target InfoTheory +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend.internal". +Scanning dependencies of target rdInfoTheory +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp +[ 8%] Linking CXX executable testDict +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 8%] Built target testDict make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend @@ -2740,30 +2777,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 8%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/Data/cQuantize.cpp -[ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 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/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_BitOps.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Built target RDGeometryLib -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend -make[4]: Entering directory 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/depend.internal". -Scanning dependencies of target GraphMol -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.cpp -[ 8%] Linking CXX executable testFPB -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -[ 8%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2782,10 +2795,12 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 8%] Linking CXX executable testFPB +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2807,69 +2822,22 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 8%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 8%] Built target testFPB -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend.internal". -Scanning dependencies of target Alignment -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build +[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_BitOps.cpp +[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_FPB.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 8%] Built target rdMetricMatrixCalc -[ 8%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/AlignPoints.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= -[ 8%] Linking CXX executable testMultiFPB -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -Scanning dependencies of target geometryTestsCatch -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/catch_tests.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Built target testMultiFPB -make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/depend.internal". -Scanning dependencies of target testGrid -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/testGrid.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp +[ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 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/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2891,6 +2859,14 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 8%] Built target RDGeometryLib +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/depend.internal". In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2909,9 +2885,33 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +Scanning dependencies of target GraphMol +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 8%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.cpp +[ 8%] Linking CXX executable testMultiFPB +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 8%] Built target testMultiFPB +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend.internal". +Scanning dependencies of target Alignment +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 8%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/AlignPoints.cpp +[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_Utils.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2925,8 +2925,8 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/ML/Data/cQuantize.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2947,72 +2947,15 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_BitOps.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 8%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Built target cQuantize -make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/depend.internal". -Scanning dependencies of target testTransforms -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/testTransforms.cpp -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_FPB.cpp -[ 8%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2020.09.4 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 8%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/LeaderPicker.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Built target Alignment -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend.internal". -Scanning dependencies of target rdGeometry -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/Point.cpp -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_Utils.cpp -[ 8%] Linking CXX executable testGrid -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/UniformGrid3D.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Built target testGrid -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/depend.internal". -Scanning dependencies of target testConrec -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/testConrec.cpp -[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp +[ 8%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3027,7 +2970,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_FPB.cpp:10: + from /build/reproducible-path/rdkit-202009.4/Code/ML/Data/cQuantize.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -3048,13 +2991,15 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_BitOps.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 9%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3068,16 +3013,14 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_Utils.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 8%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3091,31 +3034,47 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_FPB.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 9%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2020.09.4 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Built target testTransforms -make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend +[ 9%] Built target Alignment +make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend.internal". -Scanning dependencies of target testAlignment +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend.internal". +Scanning dependencies of target geometryTestsCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build +make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/testAlignment.cpp -[ 9%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 9%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/catch_tests.cpp +make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/depend.internal". +Scanning dependencies of target testGrid +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 9%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/testGrid.cpp +[ 9%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread +[ 9%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3129,26 +3088,29 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/Point.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap/wrap_Utils.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryAtom.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 9%] Built target testDataStructs -make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend +[ 9%] Built target cQuantize +make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend.internal". -Scanning dependencies of target rdAlignment +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/depend.internal". +Scanning dependencies of target testTransforms make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build +make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 9%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/testTransforms.cpp +[ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryAtom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3163,40 +3125,35 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/UniformGrid3D.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 9%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap/rdAlignment.cpp -[ 9%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp -[ 9%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp -[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp -[ 11%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/rdGeometry.cpp -[ 11%] Linking CXX executable testAlignment -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend.internal". +Scanning dependencies of target rdGeometry make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 11%] Built target testAlignment -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend.internal". -Scanning dependencies of target ChemicalFeatures +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= +[ 9%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/Point.cpp +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/depend.internal". +Scanning dependencies of target testConrec make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 11%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/FreeChemicalFeature.cpp +[ 9%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/testConrec.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3211,13 +3168,49 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 10%] Linking CXX executable testDataStructs +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 10%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/UniformGrid3D.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 10%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 +[ 10%] Built target testDataStructs +make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKithc.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend.internal". +Scanning dependencies of target testAlignment +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 10%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/testAlignment.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 10%] Built target rdSimDivPickers +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend.internal". +Scanning dependencies of target rdAlignment +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 10%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap/rdAlignment.cpp +[ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryBond.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3231,11 +3224,39 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Bond.cpp +[ 10%] Linking CXX executable testTransforms +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 10%] Linking CXX executable testGrid +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 10%] 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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend.internal". +Scanning dependencies of target ChemicalFeatures +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 10%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/FreeChemicalFeature.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 10%] Built target testGrid +[ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolOps.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3250,30 +3271,21 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/Point.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryBond.cpp -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Bond.cpp -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolOps.cpp -[ 11%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +[ 10%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindRings.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 11%] Built target rdInfoTheory -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o +[ 10%] Built target rdInfoTheory +[ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindRings.cpp +[ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -3288,18 +3300,24 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/rdGeometry.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/UniformGrid3D.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 11%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +[ 10%] Linking CXX executable testAlignment +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 10%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 +[ 10%] Built target testAlignment /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so +[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RWMol.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3313,83 +3331,101 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 11%] Built target ChemicalFeatures make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RWMol.cpp Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend.internal". Scanning dependencies of target testChemicalFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 12%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +[ 11%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/testChemicalFeatures.cpp -[ 12%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 +[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PeriodicTable.cpp +/build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': +/build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindRings.cpp:1367:36: warning: unused parameter 'mol' [-Wunused-parameter] + 1367 | void findRingFamilies(const ROMol &mol) { + | ~~~~~~~~~~~~~^~~ +[ 12%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/rdGeometry.cpp +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/atomic_data.cpp [ 12%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKithc.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 12%] Built target rdSimDivPickers -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 12%] Built target rdAlignment -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PeriodicTable.cpp -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/atomic_data.cpp -[ 12%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 12%] Built target rdGeometry [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/QueryOps.cpp -/build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': -/build/reproducible-path/rdkit-202009.4/Code/GraphMol/FindRings.cpp:1367:36: warning: unused parameter 'mol' [-Wunused-parameter] - 1367 | void findRingFamilies(const ROMol &mol) { - | ~~~~~~~~~~~~~^~~ -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. 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-I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp [ 13%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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+[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC 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CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/BondIterators.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 13%] Built target cDataStructs [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Aromaticity.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Kekulize.cpp -[ 14%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 14%] Built target rdBase +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap/rdGeometry.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 14%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDiscriminators.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 14%] Built target rdGeometry +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ConjugHybrid.cpp +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/AddHs.cpp +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Matrices.cpp /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp: In instantiation of 'static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = int; std::istream = std::basic_istream]': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1139:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int) [with T = int; std::istream = std::basic_istream]' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:928:59: required from here @@ -3400,12 +3436,6 @@ /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1139:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int) [with T = unsigned char; std::istream = std::basic_istream]' /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:930:65: required from here /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.cpp:1684:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ConjugHybrid.cpp -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/AddHs.cpp -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Matrices.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Chirality.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o @@ -3414,12 +3444,17 @@ cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Renumber.cpp +[ 15%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/AdjustQuery.cpp +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Resonance.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/StereoGroup.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 15%] Built target rdBase [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/new_canon.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o @@ -3441,19 +3476,14 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 15%] Linking CXX executable pickersTestsCatch -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 15%] Built target pickersTestsCatch -[ 15%] Linking CXX executable geometryTestsCatch -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 16%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2020.09.4 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 16%] Linking CXX executable pickersTestsCatch +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../../lib/libRDKitSimDivPickers.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKithc.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 16%] Built target geometryTestsCatch +[ 16%] Built target pickersTestsCatch cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 16%] Built target GraphMol @@ -3466,137 +3496,158 @@ cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend +make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend.internal". -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend.internal". -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend.internal". -Scanning dependencies of target Trajectory +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend.internal". -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build -Scanning dependencies of target PartialCharges +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend.internal". Scanning dependencies of target SubstructMatch -Scanning dependencies of target MolCatalog +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend.internal". +Scanning dependencies of target MolInterchange +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend.internal". +Scanning dependencies of target PartialCharges +Scanning dependencies of target rdqueries +Scanning dependencies of target Subgraphs make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Scanning dependencies of target Subgraphs make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend.internal". -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend.internal". -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend -Scanning dependencies of target MolTransforms make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Scanning dependencies of target MolInterchange -Scanning dependencies of target SmilesParse +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend.internal". +Scanning dependencies of target SLNParse +Scanning dependencies of target Trajectory make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build -[ 17%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -[ 17%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target rdChemicalFeatures +Scanning dependencies of target MolCatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerCharges.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructUtils.cpp -Scanning dependencies of target SLNParse -[ 17%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build -[ 17%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build -[ 17%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend.internal". -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.cpp -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend.internal". -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerParams.cpp +make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target SmilesParse make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory/Trajectory.cpp -[ 17%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build +[ 16%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o +[ 16%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o +[ 16%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd 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/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Parser.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructMatch.cpp +[ 16%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD 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Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -Scanning dependencies of target rdqueries -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build Scanning dependencies of target CIPLabeler -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Parser.cpp -[ 17%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 16%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/SubstructUtils.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build +Scanning dependencies of target MolTransforms +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/SubgraphUtils.cpp -[ 17%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o +[ 17%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o +make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build +[ 17%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerCharges.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build -[ 17%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParse.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/MolTransforms.cpp [ 17%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.cpp +[ 18%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/MolTransforms.cpp +[ 18%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogParams.cpp -[ 19%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNAttribs.cpp -[ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/GasteigerParams.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3618,46 +3669,35 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 19%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/MolCatalogParams.cpp +[ 19%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2020.09.4 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 19%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 20%] Built target Trajectory -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= -[ 20%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend.internal". -Scanning dependencies of target rdChemicalFeatures -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 20%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp -[ 20%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -[ 20%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 20%] Built target Subgraphs +[ 19%] Built target Trajectory 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend.internal". -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so Scanning dependencies of target Optimizer make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 20%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o +[ 19%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/BFGSOpt.cpp -[ 20%] Built target MolCatalog +[ 19%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/SLNAttribs.cpp +[ 19%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 19%] Built target MolCatalog make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= @@ -3667,29 +3707,19 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 20%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o +[ 19%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Trajectory.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 20%] Built target PartialCharges -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap 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rdPartialCharges -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 20%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -[ 21%] Linking CXX executable testConrec -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 -[ 21%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o +[ 19%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o +cd 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-std=gnu++11 -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/SubgraphUtils.cpp +[ 19%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Queries.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 19%] Linking CXX executable geometryTestsCatch +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 19%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/LinearSearch.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 21%] Built target testConrec +[ 19%] Built target geometryTestsCatch 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= @@ -3699,18 +3729,10 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 21%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o +[ 19%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o +[ 19%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesParseOps.cpp -[ 21%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/LinearSearch.cpp -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.cpp -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.cpp -[ 21%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Writer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3724,22 +3746,63 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +[ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 20%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 20%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2020.09.4 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 21%] Built target SubstructMatch -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.cpp +[ 20%] Built target SubstructMatch +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so +[ 20%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/sln.tab.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 20%] Built target Optimizer +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend.internal". +Scanning dependencies of target testOptimizer +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build +[ 20%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 +[ 21%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/testOptimizer.cpp +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 21%] Built target PartialCharges +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/depend.internal". +Scanning dependencies of target ForceField +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 21%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/ForceField.cpp +[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3775,15 +3838,76 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Queries.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 21%] Built target MolTransforms +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= +[ 21%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend.internal". +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2020.09.4 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +Scanning dependencies of target rdPartialCharges +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 21%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 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--verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2020.09.4 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 22%] Built target MolInterchange +make -f 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend.internal". +Scanning dependencies of target rdMolTransforms +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 22%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp +[ 22%] Built target testConrec +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend.internal". +Scanning dependencies of target ShapeHelpers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 22%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp +[ 22%] Linking CXX executable testOptimizer +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 22%] Built target testOptimizer +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend.internal". +Scanning dependencies of target rdMolInterchange +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 22%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3797,45 +3921,49 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Queries.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.h:15, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp:5: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp -[ 21%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2020.09.4 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 21%] Built target MolTransforms -[ 21%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend.internal". +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.cpp Scanning dependencies of target MolAlign make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 21%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o +[ 22%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so +cd 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.cpp +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3849,37 +3977,14 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.h:15, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp:5: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 21%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/lex.yysln.cpp -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -[ 21%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 21%] Built target rdPartialCharges -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend.internal". -Scanning dependencies of target testOptimizer -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 22%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer/testOptimizer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3893,14 +3998,22 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdTrajectory.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202009.4/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-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 22%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp +[ 22%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdTrajectory.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3915,87 +4028,61 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmartsWrite.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/CXSmilesOps.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/smarts.tab.cpp +[ 22%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 22%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 22%] Built target rdPartialCharges [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 23%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 23%] Built target rdtrajectory -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend -make[4]: Entering directory 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-I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/ForceField.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c 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object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 23%] Built target testOptimizer -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend.internal". -Scanning dependencies of target rdMolTransforms -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 23%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so +[ 24%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2020.09.4 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 23%] Built target MolAlign -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend +[ 24%] Built target SLNParse +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend.internal". -Scanning dependencies of target ShapeHelpers +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend.internal". +Scanning dependencies of target rdSLNParse make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build +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-202009.4/obj-x86_64-linux-gnu' -[ 23%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +[ 24%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionAngle.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +[ 24%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -[ 23%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 23%] Built target rdChemicalFeatures +[ 24%] Built target MolAlign make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= @@ -4005,34 +4092,8 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 23%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o +[ 24%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/RDDepictor.cpp -[ 23%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 23%] Built target rdMolCatalog -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend.internal". -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -Scanning dependencies of target rdCoordGen -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 23%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap/rdCoordGen.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2020.09.4 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 23%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 -[ 23%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/AngleBend.cpp -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4046,65 +4107,86 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdTrajectory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2020.09.4 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so +[ 24%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 24%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 23%] Built target MolInterchange -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend +[ 24%] Built target rdMolInterchange +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend.internal". -Scanning dependencies of target rdMolInterchange -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2020.09.4 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend.internal". +Scanning dependencies of target rdCoordGen make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build +make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o +[ 24%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap/rdCoordGen.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 24%] Built target rdMolCatalog +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp -[ 24%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp +[ 25%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 24%] Built target SLNParse -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend +[ 25%] Built target rdtrajectory +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/DistanceConstraint.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/AngleConstraint.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 25%] Built target ShapeHelpers +make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend.internal". -Scanning dependencies of target rdSLNParse +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend.internal". +Scanning dependencies of target rdShapeHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 24%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c 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-isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp -[ 24%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 25%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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-fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmilesWrite.cpp +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/SmartsWrite.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Nonbonded.cpp -[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/lex.yysmarts.cpp -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Inversion.cpp +[ 26%] Built target rdMolTransforms +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionConstraint.cpp +[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/CXSmilesOps.cpp +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/PositionConstraint.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4119,17 +4201,25 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap/rdCoordGen.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp:35: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/lex.yysmiles.cpp -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionAngle.cpp +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Params.cpp +[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/smarts.tab.cpp +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/AngleBend.cpp +[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/smiles.tab.cpp +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.cpp +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/StretchBend.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4144,15 +4234,31 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp:35: + from /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap/rdCoordGen.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/DistanceConstraint.cpp +[ 27%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 27%] Built target rdqueries +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/OopBend.cpp +[ 27%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 27%] Built target CIPLabeler +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4167,259 +4273,44 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp:10: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend.internal". /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/TorsionConstraint.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 26%] Built target CIPLabeler -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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Scanning dependencies of target rdCIPLabeler make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp -[ 26%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/EmbeddedFrag.cpp -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/Params.cpp -[ 26%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 26%] Built target ShapeHelpers -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= -[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend.internal". -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -Scanning dependencies of target rdShapeHelpers -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 27%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC 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-shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/BondStretch.cpp -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/StretchBend.cpp -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/OopBend.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 29%] Built target rdSLNParse -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionAngle.cpp -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +[ 28%] Built target rdSLNParse +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Nonbonded.cpp -[ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 29%] Built target rdMolInterchange -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/DistanceConstraint.cpp -[ 29%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/TorsionConstraint.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 -[ 29%] Built target SmilesParse -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake 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'/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 29%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/cptest.cpp -[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/Params.cpp -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/MolFragmenter.cpp -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend -[ 30%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/querytest.cpp -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/depend.internal". -Scanning dependencies of target test-valgrind -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/test-valgrind.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend.internal". -Scanning dependencies of target graphmolIterTest -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/itertest.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp:13: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend.internal". -Scanning dependencies of target graphmolMemTest1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= -[ 30%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/memtest1.cpp -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend.internal". -Scanning dependencies of target smaTest1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend -[ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/smatest.cpp -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend.internal". -Scanning dependencies of target smiTest2 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/test2.cpp -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend.internal". -Scanning dependencies of target Fingerprints -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.cpp -[ 31%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/PatternFingerprints.cpp -[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so 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/usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 29%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/EmbeddedFrag.cpp +[ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/lex.yysmarts.cpp +[ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/lex.yysmiles.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h:36, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:13: @@ -4460,85 +4351,218 @@ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ -[ 31%] Built target rdCIPLabeler -make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend +[ 30%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/DepictUtils.cpp +[ 30%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 30%] Built target rdCoordGen +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 30%] Built target rdShapeHelpers +[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 30%] Built target rdCIPLabeler +[ 30%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 30%] Built target SmilesParse +make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend.internal". -Scanning dependencies of target FilterCatalog +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend +Scanning dependencies of target graphmolcpTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Filters.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend.internal". +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/depend.internal". +Scanning dependencies of target ChemTransforms +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 32%] Built target Depictor +Scanning dependencies of target test-valgrind +Scanning dependencies of target graphmolqueryTest +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend.internal". +make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 30%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/cptest.cpp +Scanning dependencies of target graphmolIterTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend.internal". +Scanning dependencies of target smiTest2 +Scanning dependencies of target graphmolMemTest1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target smaTest1 +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build +[ 30%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/ChemTransforms.cpp +[ 30%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/itertest.cpp 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-202009.4/obj-x86_64-linux-gnu' +cd 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-I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/memtest1.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu 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-I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/test2.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/smatest.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu 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Scanning dependencies of target testSubgraphs2 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/test2.cpp -[ 33%] Linking CXX executable graphmolIterTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 33%] Built target graphmolIterTest -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend.internal". 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-I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs/test1.cpp -[ 33%] Linking CXX executable graphmolcpTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 33%] Linking CXX executable test-valgrind -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -o test-valgrind 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'/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target Fingerprints make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 34%] Built target graphmolcpTest make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend +[ 31%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Scanning dependencies of target FragCatalog -[ 34%] Built target test-valgrind make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Fingerprints.cpp +[ 32%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +[ 32%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2020.09.4 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 32%] Built target ForceField +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= -[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp Dependee 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Scanning dependencies of target testPartialCharges make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 34%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o +[ 32%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/test1.cpp +[ 32%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat 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../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 34%] Built target smiTest2 +[ 32%] Built target Depictor 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= @@ -4548,29 +4572,34 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o +[ 32%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 34%] Built target rdShapeHelpers +[ 33%] Built target smiTest2 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend.internal". +[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalog.cpp Scanning dependencies of target testCIPLabeler make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o +[ 33%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 33%] Linking CXX executable testSubgraphs2 +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 33%] Linking CXX executable testPartialCharges +cd 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Built target testSubgraphs2 make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= @@ -4580,14 +4609,10 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make 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-isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp -[ 34%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2020.09.4 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o 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-I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.cpp -[ 34%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/Abbreviations.cpp +[ 33%] Linking CXX executable graphmolIterTest Scanning dependencies of target FileParsers +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 34%] Built target testPartialCharges +[ 33%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 +[ 33%] Built target graphmolIterTest 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-202009.4/obj-x86_64-linux-gnu' cd 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'/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= @@ -4672,13 +4686,54 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 34%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o +[ 33%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 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CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 34%] Built target graphmolqueryTest +[ 33%] Built target testSubgraphs1 +[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp +[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatGenerator.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 34%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileParser.cpp +[ 34%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp +[ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp +[ 34%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so +cd 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+cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 34%] Built target ChemTransforms 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdchem.cpp -[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatGenerator.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 34%] Built target ReducedGraphs +[ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp +[ 34%] Linking CXX executable graphmolqueryTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 34%] Built target graphmolqueryTest 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend.internal". +[ 34%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp Scanning dependencies of target testReducedGraphs make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp -[ 34%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp -[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MACCS.cpp -[ 34%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp -[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganFingerprints.cpp +[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp +[ 34%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD 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CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/CIPMol.cpp +[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 35%] Built target rdDepictor +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend.internal". +Scanning dependencies of target rdReducedGraphs +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 35%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4761,36 +4816,23 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp -[ 34%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileParser.cpp -[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp -[ 35%] Linking CXX executable testReducedGraphs +[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +[ 36%] Linking CXX executable testReducedGraphs cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 -[ 35%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2020.09.4 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 35%] Built target testReducedGraphs -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= +[ 36%] Built target testReducedGraphs +[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 36%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2020.09.4 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/FilterMatchers.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2020.09.4 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend.internal". -Scanning dependencies of target rdReducedGraphs -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 35%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp -[ 35%] Built target Abbreviations +[ 36%] Built target Abbreviations make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make 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'/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 35%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o +[ 36%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAbbreviations_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp -[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 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/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4852,76 +4865,34 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp +[ 36%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 38%] Built target MolChemicalFeatures -[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 39%] Built target FragCatalog -[ 40%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o +[ 36%] Built target MolChemicalFeatures +[ 37%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 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CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 40%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o 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../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +[ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragCatParams.cpp +[ 37%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2020.09.4 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-I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairs.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 40%] Built target FilterCatalog +[ 37%] Built target testSLNParse 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= @@ -4931,17 +4902,8 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 41%] Building CXX object 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-fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 42%] Built target rdAbbreviations -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4956,16 +4918,28 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Table.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +[ 38%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 38%] Built target rdReducedGraphs +[ 38%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp +[ 38%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolFileStereochem.cpp +[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MACCS.cpp +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MHFP.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4980,42 +4954,13 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Atom.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Table.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend.internal". -Scanning dependencies of target rdfiltercatalog /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 43%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp -[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.cpp -[ 43%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 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 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 43%] Built target ForceFieldHelpers -make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/depend.internal". -Scanning dependencies of target DistGeometry -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistGeomUtils.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.cpp:14: /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h: In function 'std::string RDKit::SGroupWriting::BuildV2000SAPLines(int, const RDKit::SubstanceGroup&)': /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MolSGroupWriting.h:24:25: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size 4 [-Wformat-truncation=] @@ -5046,10 +4991,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5071,6 +5012,47 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 38%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp +[ 38%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 38%] Built target FilterCatalog +[ 39%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 39%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +[ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Atom.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp +[ 40%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend.internal". +Scanning dependencies of target rdfiltercatalog +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 40%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5084,15 +5066,36 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.h:36, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp:32: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/MorganGenerator.cpp +[ 40%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 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 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 41%] Built target rdAbbreviations +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 42%] Built target ForceFieldHelpers +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/depend.internal". +Scanning dependencies of target DistGeometry +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5107,33 +5110,34 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Bond.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Atom.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -[ 43%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Mol.cpp -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SDMolSupplier.cpp -[ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.cpp -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.cpp -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 42%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistGeomUtils.cpp +[ 43%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 43%] Built target FragCatalog +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend.internal". +Scanning dependencies of target rdForceField +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 43%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap/ForceField.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5148,15 +5152,17 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Mol.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/TriangleSmooth.cpp +[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/FingerprintUtil.cpp +[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Node.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5170,8 +5176,9 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.h:36, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp:32: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -5192,44 +5199,32 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Bond.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 44%] Built target Fingerprints -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend +[ 43%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp +[ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SDMolSupplier.cpp +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend.internal". -Scanning dependencies of target rdForceField +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend.internal". +Scanning dependencies of target rdForceFieldHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 44%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap/ForceField.cpp -[ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistViolationContrib.cpp -[ 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CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -[ 45%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SmilesWriter.cpp -[ 46%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TDTMolSupplier.cpp -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Conformer.cpp -[ 46%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TDTWriter.cpp -[ 46%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2020.09.4 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend.internal". -Scanning dependencies of target rdMHFPFingerprint -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 46%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 46%] Built target DistGeometry -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend.internal". -Scanning dependencies of target rdFingerprintGenerator -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 47%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Edge.cpp +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend.internal". -Scanning dependencies of target rdForceFieldHelpers +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend.internal". +Scanning dependencies of target O3AAlign make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build +make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +[ 44%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5330,17 +5273,15 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TplFileParser.cpp -[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/RingInfo.cpp +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SDWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5355,35 +5296,25 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Conformer.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 49%] Linking CXX executable testCIPLabeler -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TplFileWriter.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PDBParser.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 49%] Built target testCIPLabeler -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend.internal". -Scanning dependencies of target O3AAlign -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 49%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp -[ 49%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp +[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Sort.cpp +[ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/TriangleSmooth.cpp +[ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Mol.cpp +[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SmilesWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5405,6 +5336,43 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TDTMolSupplier.cpp +[ 44%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/DistViolationContrib.cpp +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 44%] Built target Fingerprints +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend.internal". +Scanning dependencies of target rdMHFPFingerprint +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 44%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 44%] Built target rdMolChemicalFeatures +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend.internal". +Scanning dependencies of target rdFingerprintGenerator +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 45%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5418,13 +5386,26 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Mol.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TDTWriter.cpp +[ 46%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/ChiralViolationContrib.cpp +[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Conformer.cpp +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TplFileParser.cpp +[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/RingInfo.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5438,15 +5419,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PDBWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5460,16 +5439,34 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/RingInfo.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PDBSupplier.cpp +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/TplFileWriter.cpp +[ 47%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2020.09.4 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 47%] Built target DistGeometry +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend.internal". +Scanning dependencies of target SubstructLibrary +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 47%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +[ 47%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5484,40 +5481,23 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Conformer.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 47%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/XYZFileWriter.cpp -[ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MaeMolSupplier.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 49%] Built target rdMolChemicalFeatures -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend.internal". -Scanning dependencies of target SubstructLibrary -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 49%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -[ 49%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/EditableMol.cpp -[ 49%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 47%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/PDBParser.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 49%] Built target rdForceField +[ 47%] Built target O3AAlign make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= @@ -5526,13 +5506,27 @@ Scanning dependencies of target DistGeomHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 49%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 47%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/ProximityBonds.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.cpp +[ 47%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 47%] Built target rdForceFieldHelpers +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/depend.internal". +Scanning dependencies of target testDistGeom +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 47%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/testDistGeom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5547,41 +5541,20 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/EditableMol.cpp:17: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/RingInfo.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceWriters.cpp -[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 50%] Built target rdForceFieldHelpers -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/depend.internal". -Scanning dependencies of target testDistGeom -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 50%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/DistGeom/testDistGeom.cpp -[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MonomerInfo.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SVGParser.cpp -[ 50%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +[ 47%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 50%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 53%] Built target testDistGeom -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp +[ 50%] Built target testDistGeom +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/EditableMol.cpp +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MonomerInfo.cpp +[ 50%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 50%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/DistGeom/Wrap/DistGeom.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 50%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 50%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 50%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MaeMolSupplier.cpp +[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/ProximityBonds.cpp +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 50%] Built target rdFingerprintGenerator +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SequenceParsers.cpp +[ 51%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/Rule6.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5634,10 +5648,11 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp -[ 53%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o +[ 51%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Embedder.cpp +[ 51%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5652,17 +5667,49 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/DistGeom/Wrap/DistGeom.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/EditableMol.cpp:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +[ 51%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 51%] Built target DistGeom +[ 51%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/PatternFactory.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c 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../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 51%] Built target rdMHFPFingerprint +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/SVGParser.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp +[ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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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 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl [ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ 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'/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 53%] Built target testCIPLabeler +[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5683,6 +5730,23 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 54%] Built target SubstructLibrary +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend.internal". +Scanning dependencies of target rdSubstructLibrary +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5703,20 +5767,13 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 53%] Built target rdMHFPFingerprint -[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp -[ 53%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 53%] Built target DistGeom -[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/Chirality.cpp +[ 54%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp +[ 54%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp +[ 54%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5730,13 +5787,16 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/StereoGroup.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 54%] Built target DistGeomHelpers In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5750,25 +5810,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/StereoGroup.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 54%] Built target SubstructLibrary -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend.internal". -Scanning dependencies of target rdSubstructLibrary In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5787,156 +5835,9 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp -[ 54%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp -[ 54%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 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/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.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/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 54%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 54%] Built target DistGeomHelpers -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 54%] 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend.internal". -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build -Scanning dependencies of target chiralityTestsCatch -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake" is newer than depender 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend.internal". -Scanning dependencies of target graphmoltestPicklerGlobalSetting -Scanning dependencies of target graphmolTestsCatch -Scanning dependencies of target graphmoltestChirality -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build -Scanning dependencies of target graphmolAdjustQueryCatch -make[4]: 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_sgroups.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 55%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -cd 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_chirality.cpp -[ 55%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testSGroup.cpp -make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build -[ 55%] Building CXX object 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CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202009.4/External/CoordGen/test.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testPicklerGlobalSettings.cpp -[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_graphmol.cpp -[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_adjustquery.cpp -[ 56%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 56%] Built target rdfiltercatalog -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend.internal". -Scanning dependencies of target graphmolTest1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/test1.cpp -[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5950,8 +5851,9 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:31: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.h:36, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp:32: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -5971,17 +5873,19 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.h:36, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp:32: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp +[ 55%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 55%] Built target rdfiltercatalog In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:34: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] @@ -5993,17 +5897,166 @@ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ +[ 55%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 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/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.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/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 55%] Built target FileParsers +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend +make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend +make[4]: Entering directory 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend.internal". +Scanning dependencies of target graphmoltestPicklerGlobalSetting +Scanning dependencies of target graphmoltestChirality +Scanning dependencies of target testSGroup +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build +Scanning dependencies of target graphmolTest1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend.internal". +Scanning dependencies of target graphmolSGroupCatch +Scanning dependencies of target graphmolTestsCatch +Scanning dependencies of target chiralityTestsCatch +Scanning dependencies of target graphmolAdjustQueryCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build Scanning dependencies of target resMolSupplierTest +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target graphmoltestPickler +make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testPicklerGlobalSettings.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target graphmolMolOpsTest make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testSGroup.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testChirality.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_chirality.cpp +Scanning dependencies of target testMMFFForceField +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_sgroups.cpp +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o +Scanning dependencies of target testCoordGen +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_graphmol.cpp +Scanning dependencies of target testUFFForceField +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/test1.cpp +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/resMolSupplierTest.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testPickler.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_adjustquery.cpp +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o +[ 55%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/molopstest.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF/testMMFFForceField.cpp +[ 55%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202009.4/External/CoordGen/test.cpp +[ 56%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF/testUFFForceField.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RDKitBase.h:25, from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SubstanceGroup.cpp:17: @@ -6017,45 +6070,11 @@ /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:58:55: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] 58 | : Point(other), x(other.x), y(other.y), z(other.z) {} | ~~~~~~^ -[ 56%] Linking CXX executable testCoordGen -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 56%] Built target testCoordGen -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend.internal". -Scanning dependencies of target graphmoltestPickler -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testPickler.cpp -[ 56%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 56%] Built target graphmoltestPicklerGlobalSetting -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend.internal". -Scanning dependencies of target graphmolMolOpsTest -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 56%] Linking CXX executable testUFFForceField -[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/molopstest.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 57%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp -[ 57%] Built target testUFFForceField +[ 57%] Built target resMolSupplierTest make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= @@ -6070,14 +6089,11 @@ [ 57%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 57%] Linking CXX executable testSGroup -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 58%] Linking CXX executable resMolSupplierTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 57%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 58%] Built target rdSubstructLibrary +[ 57%] Built target rdSubstructLibrary make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= @@ -6085,75 +6101,83 @@ Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/depend.internal". Scanning dependencies of target molBundleTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 58%] Built target resMolSupplierTest +[ 58%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/testMolBundle.cpp +[ 58%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 58%] Built target rdchem 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= -[ 59%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend.internal". 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../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 58%] Linking CXX executable testCoordGen +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script 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../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 59%] Built target testMMFFForceField +[ 58%] Built target testCoordGen make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend.internal". +[ 58%] Linking CXX executable testUFFForceField +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 Scanning dependencies of target smiTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build -[ 59%] Built target rdchem make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/catch_tests.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 58%] Built target testUFFForceField 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= -[ 59%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend.internal". -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/catch_tests.cpp Scanning dependencies of target cxsmilesTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 60%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o +[ 59%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse/cxsmiles_test.cpp -[ 60%] Linking CXX executable graphmolTest1 -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp +[ 60%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp +[ 60%] Linking CXX executable molBundleTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 60%] Linking CXX executable testSGroup +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 60%] Built target graphmolTest1 +[ 60%] Built target molBundleTest make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= @@ -6165,11 +6189,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolWriter.cpp -[ 61%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 61%] Built target hanoiTest +[ 61%] Built target testSGroup 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= @@ -6181,6 +6202,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testSequence.cpp +[ 62%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 62%] Built target hanoiTest 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= @@ -6192,11 +6218,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/test1.cpp -[ 62%] Linking CXX executable molBundleTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 62%] Linking CXX executable graphmolTest1 +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../lib/libRDKitForceField.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 62%] Built target molBundleTest +[ 62%] Built target graphmolTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= @@ -6208,11 +6234,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp -[ 62%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 62%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp +[ 62%] Linking CXX executable testDepictor +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 62%] Built target testSequence +[ 62%] Built target testDepictor 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= @@ -6222,36 +6250,32 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 62%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp -[ 62%] Linking CXX executable testDepictor -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 62%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 62%] Built target testDepictor +[ 62%] Built target testMMFFForceField 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend.internal". +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Scanning dependencies of target testExtendedStereoParsing make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -/build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp: In function 'void testGitHub3517()': -/build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp:2805:10: warning: unused variable 'l' [-Wunused-variable] - 2805 | size_t l = sdsup.length(); - | ^ -[ 62%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 62%] Built target graphmoltestChirality +[ 62%] Built target testSequence 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake --color= +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend.internal". Scanning dependencies of target testGeneralFileReader @@ -6260,6 +6284,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testGeneralFileReader.cpp +[ 62%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp [ 62%] Linking CXX executable cxsmilesTest cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so @@ -6276,11 +6302,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testTpls.cpp -[ 63%] Linking CXX executable testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 63%] Linking CXX executable graphmoltestPickler +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +/build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp: In function 'void testGitHub3517()': +/build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMolSupplier.cpp:2805:10: warning: unused variable 'l' [-Wunused-variable] + 2805 | size_t l = sdsup.length(); + | ^ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 63%] Built target testExtendedStereoParsing +[ 63%] Built target graphmoltestPickler 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= @@ -6292,11 +6322,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 63%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 64%] Linking CXX executable testExtendedStereoParsing +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 63%] Built target testMultithreadedMolSupplier +[ 64%] Built target testExtendedStereoParsing 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= @@ -6306,13 +6336,13 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o +[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 64%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 64%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 64%] Built target graphmoltestPickler +[ 64%] Built target graphmoltestChirality make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= @@ -6324,11 +6354,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/testPropertyLists.cpp -[ 64%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 64%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 64%] Built target testMolWriter +[ 64%] Built target testMultithreadedMolSupplier 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= @@ -6340,14 +6370,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/test1.cpp +[ 64%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so [ 64%] Linking CXX executable testTplParser cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 65%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 65%] Built target testTplParser +[ 64%] Built target testMol2ToMol 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake --color= @@ -6357,10 +6387,10 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o +[ 64%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct/catch_tests.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 65%] Built target testGeneralFileReader +[ 64%] Built target testTplParser 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= @@ -6370,13 +6400,13 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o +[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Crippen.cpp -[ 65%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 65%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 65%] Built target testMol2ToMol +[ 65%] Built target testGeneralFileReader make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= @@ -6388,11 +6418,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -[ 66%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -o graphmolTestsCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 65%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= @@ -6402,13 +6432,20 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' 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-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o +[ 65%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -o graphmolSGroupCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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-DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/BCUT.cpp +[ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/catch_main.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPropertyLists.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/catch_main.cpp +[ 65%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 65%] Linking CXX executable testMolSupplier +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target graphmolSGroupCatch +[ 65%] Built target smiTest1 make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= @@ -6418,17 +6455,10 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o +[ 65%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/BCUT.cpp -[ 66%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPropertyLists.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/catch_main.cpp -[ 66%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target smiTest1 +[ 65%] Built target testMolSupplier 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= @@ -6438,16 +6468,13 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o +[ 65%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/test1.cpp -[ 66%] Linking CXX executable testSubstructMatch +[ 65%] Linking CXX executable testSubstructMatch cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 66%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target testSubstructMatch +[ 65%] Built target testSubstructMatch 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= @@ -6457,10 +6484,13 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o +[ 65%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp +[ 65%] Linking CXX executable testChemTransforms +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target filterCatalogTest +[ 65%] Built target testChemTransforms make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= @@ -6470,16 +6500,18 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o +[ 65%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 66%] Linking CXX executable testMolSupplier -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDStreams.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 66%] Linking CXX executable graphmolAdjustQueryCatch +[ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/catch_main.cpp +[ 65%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o CMakeFiles/graphmolSGroupCatch.dir/catch_main.cpp.o -o graphmolSGroupCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 65%] Linking CXX executable graphmolAdjustQueryCatch cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_main.cpp.o -o graphmolAdjustQueryCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target testMolSupplier +[ 65%] Built target graphmolSGroupCatch 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= @@ -6488,24 +6520,6 @@ Scanning dependencies of target testFingerprintGenerators make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target graphmolAdjustQueryCatch -make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend.internal". -Scanning dependencies of target fpTestCatch -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/catch_tests.cpp -[ 66%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers/catch_main.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6525,16 +6539,34 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o +[ 65%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 65%] Built target graphmolAdjustQueryCatch +make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend.internal". +Scanning dependencies of target fpTestCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 65%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/catch_tests.cpp +[ 65%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp -[ 66%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 65%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target testFragCatalog +[ 65%] Built target filterCatalogTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= @@ -6544,13 +6576,13 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o +[ 65%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/test1.cpp -[ 66%] Linking CXX executable testMHFPFingerprint -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 65%] Linking CXX executable testFragCatalog +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target testMHFPFingerprint +[ 65%] Built target testFragCatalog 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= @@ -6560,10 +6592,26 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o +[ 65%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/test1.cpp -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolDescriptors.cpp +[ 65%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 65%] Built target testMHFPFingerprint +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend.internal". +Scanning dependencies of target testMMFFForceFieldHelpersMultiThread +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolSurf.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6585,27 +6633,14 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Linking CXX executable chiralityTestsCatch +[ 65%] Linking CXX executable chiralityTestsCatch cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o -o chiralityTestsCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 66%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 66%] Built target chiralityTestsCatch -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend.internal". -Scanning dependencies of target testMMFFForceFieldHelpersMultiThread -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 66%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 -[ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target testChemTransforms make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= @@ -6617,11 +6652,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp -[ 67%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 67%] Built target fileParsersTest1 +[ 66%] Built target graphmolMolOpsTest 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= @@ -6631,33 +6663,35 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o +[ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolSurf.cpp -[ 67%] Linking CXX executable testMolTransforms +[ 66%] Linking CXX executable testMolTransforms cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 67%] Built target testMolTransforms +[ 66%] Built target testMolTransforms 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend.internal". +[ 67%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so Scanning dependencies of target testCrystalForceField make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp -[ 68%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 68%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o CMakeFiles/graphmolTestsCatch.dir/catch_main.cpp.o -o graphmolTestsCatch ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 68%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 68%] Built target testFingerprintGenerators +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 68%] Built target fileParsersTest1 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= @@ -6669,9 +6703,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp -[ 68%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend @@ -6685,6 +6716,23 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 68%] Built target graphmolTestsCatch +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend.internal". +Scanning dependencies of target testFeatures +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 68%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.cpp +[ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6706,29 +6754,11 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../lib/libRDKitDepictor.so.1.2020.09.4 ../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../lib/libRDKitAlignment.so.1.2020.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Lipinski.cpp -[ 69%] Built target graphmolMolOpsTest -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend.internal". -Scanning dependencies of target testFeatures -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 69%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp -[ 69%] Linking CXX executable testCrystalForceField +[ 68%] Linking CXX executable testCrystalForceField cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 69%] Built target testCrystalForceField +[ 68%] Built target testCrystalForceField 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= @@ -6738,14 +6768,8 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 69%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o +[ 68%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp -[ 69%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp -[ 70%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6764,92 +6788,69 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 70%] 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 69%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 69%] Built target testFingerprintGenerators +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend.internal". Scanning dependencies of target testMolCatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o +[ 69%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/test1.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp -[ 70%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 70%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 69%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 69%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Built target testUFFForceFieldHelpers +[ 69%] Built target testFeatures 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend.internal". -Scanning dependencies of target FMCS make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Built target testShapeHelpers +[ 69%] Built target smiTestCatch make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend +Scanning dependencies of target FMCS make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend.internal". Scanning dependencies of target MMPA make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o +[ 69%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o +[ 69%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/MMPA.cpp -[ 70%] Linking CXX executable smiTestCatch -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 70%] Linking CXX executable testFeatures -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/FMCS.cpp +[ 69%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp +[ 70%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Built target smiTestCatch +[ 70%] Built target testMMFFForceFieldHelpers 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= -[ 70%] Built target testFeatures -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend.internal". Scanning dependencies of target trajectoryTest @@ -6858,14 +6859,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory/trajectoryTest.cpp -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend.internal". -Scanning dependencies of target substructLibraryTest -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp In file included from /usr/include/boost/bind.hpp:30, from /usr/include/boost/property_tree/json_parser/detail/parser.hpp:7, from /usr/include/boost/property_tree/json_parser/detail/read.hpp:13, @@ -6874,16 +6867,27 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp -[ 70%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 71%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 70%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 70%] Built target testUFFForceFieldHelpers +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend.internal". +Scanning dependencies of target substructLibraryTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 70%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +[ 70%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 71%] Built target substructTestCatch +[ 70%] Built target testShapeHelpers 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= @@ -6893,13 +6897,42 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o +[ 71%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/rapidjson -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/test1.cpp +[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MQN.cpp +[ 72%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 72%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 72%] Built target testMolCatalog 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend.internal". Scanning dependencies of target rdmolfiles @@ -6908,16 +6941,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolfiles.cpp -[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MQN.cpp -[ 72%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 72%] Built target testFingerprints +[ 72%] Built target substructTestCatch 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= @@ -6929,65 +6954,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/__/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAbbreviations.dir/__/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/catch_main.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 72%] Built target rdDistGeom -[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Property.cpp -[ 74%] Linking CXX executable trajectoryTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolfiles.cpp:13: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 74%] Built target trajectoryTest -[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -[ 75%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +[ 72%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2020.09.4 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2020.09.4 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 75%] Built target MMPA +[ 72%] Built target MMPA 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= @@ -6997,52 +6969,51 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +[ 72%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/MMPA_UnitTest.cpp -[ 75%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Property.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 75%] Built target rdfragcatalog +[ 73%] Built target rdDistGeom 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 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/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 77%] Built target substructLibraryTest -[ 77%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR2D.cpp +[ 75%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 75%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp make[4]: Leaving directory 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Seed.cpp +[ 75%] Built target testFingerprints +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7057,41 +7028,29 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolfiles.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp +[ 75%] Linking CXX executable testDistGeomHelpers +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 75%] Linking CXX executable substructLibraryTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesMolSupplier.cpp -[ 77%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/SubstructMatchCustom.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp -[ 77%] Built target molInterchangeTest1 -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 285 | if (df_isTextMode && c > STD_ASCII) { - | ~~^~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 297 | if ((!df_isTextMode || c <= STD_ASCII) && - | ~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 308 | if (df_isTextMode && c > STD_ASCII && - | ~~^~~~~~~~~~~ -[ 77%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp -[ 77%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +[ 75%] Built target testDistGeomHelpers +[ 76%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7112,16 +7071,56 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -o fileParsersCatchTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 77%] Built target fileParsersCatchTest -[ 77%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.cpp -[ 77%] Linking CXX executable testMMPA +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 76%] Linking CXX executable testMMPA cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 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-fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/USRDescriptor.cpp +[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 77%] Built target testPropertyLists +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/catch_tests.cpp +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PMI.cpp +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR3D.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7136,17 +7135,53 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MaeMolSupplier.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 78%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o CMakeFiles/fileParsersCatchTest.dir/catch_main.cpp.o -o fileParsersCatchTest ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 78%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 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object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MaeMolSupplier.cpp +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDMolSupplier.cpp +In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 285 | if (df_isTextMode && c > STD_ASCII) { + | ~~^~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 297 | if ((!df_isTextMode || c <= STD_ASCII) && + | ~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 308 | if (df_isTextMode && c > STD_ASCII && + | ~~^~~~~~~~~~~ +[ 78%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 78%] Built target rdfragcatalog +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTMolSupplier.cpp +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MORSE.cpp +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.cpp +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/WHIM.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7182,13 +7217,19 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTMolSupplier.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MaeMolSupplier.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/CoulombMat.cpp +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesMolSupplier.cpp +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7203,15 +7244,13 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTMolSupplier.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 77%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MaeMolSupplier.cpp:22: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] @@ -7223,15 +7262,56 @@ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ -[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 77%] Built target rdMMPA -[ 77%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.cpp -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AtomFeat.cpp +[ 79%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 79%] 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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= +[ 79%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 79%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/testFMCS_Unit.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 79%] Built target fpTestCatch +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/PDBWriter.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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test 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-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-202009.4/obj-x86_64-linux-gnu' +[ 80%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7253,29 +7333,7 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.cpp:20: -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 285 | if (df_isTextMode && c > STD_ASCII) { - | ~~^~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 297 | if ((!df_isTextMode || c <= STD_ASCII) && - | ~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 308 | if (df_isTextMode && c > STD_ASCII && - | ~~^~~~~~~~~~~ -[ 77%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/SubstructMatchCustom.cpp -[ 77%] Linking CXX executable fpTestCatch -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/EEM.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 77%] Built target fpTestCatch -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/PDBWriter.cpp -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o +[ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -7291,13 +7349,26 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend.internal". +Scanning dependencies of target RGroupDecomposition +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +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-202009.4/obj-x86_64-linux-gnu' +[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7319,11 +7390,30 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp -[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PBF.cpp -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.cpp:21: +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp +In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SmilesWriter.cpp:20: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { @@ -7334,8 +7424,6 @@ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ -[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/PMI.cpp In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/SDWriter.cpp:21: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] @@ -7347,10 +7435,6 @@ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ -[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/AUTOCORR3D.cpp -[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/RDF.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7365,17 +7449,14 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/MORSE.cpp -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:23: +In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/TDTWriter.cpp:21: /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 285 | if (df_isTextMode && c > STD_ASCII) { @@ -7386,8 +7467,6 @@ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ -[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/GETAWAY.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7409,10 +7488,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/WHIM.cpp -[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/CoulombMat.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7427,7 +7502,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7445,79 +7520,6 @@ /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] 308 | if (df_isTextMode && c > STD_ASCII && | ~~^~~~~~~~~~~ -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:23: -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 285 | if (df_isTextMode && c > STD_ASCII) { - | ~~^~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 297 | if ((!df_isTextMode || c <= STD_ASCII) && - | ~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 308 | if (df_isTextMode && c > STD_ASCII && - | ~~^~~~~~~~~~~ -[ 80%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 80%] 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-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend.internal". -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= -Scanning dependencies of target testFMCS -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend.internal". -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend.internal". -Scanning dependencies of target rdFMCS -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build -Scanning dependencies of target RGroupDecomposition -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Scanning dependencies of target FMCStest -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build -[ 80%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/testFMCS_Unit.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 80%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -[ 80%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test/testFMCS.cpp -[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp -[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp -[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp -[ 80%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/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/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 80%] Built target rdmolfiles In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7532,45 +7534,76 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp +In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:23: +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 285 | if (df_isTextMode && c > STD_ASCII) { + | ~~^~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 297 | if ((!df_isTextMode || c <= STD_ASCII) && + | ~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 308 | if (df_isTextMode && c > STD_ASCII && + | ~~^~~~~~~~~~~ +[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp +In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedMolSupplier.h:15, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:23: +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 285 | if (df_isTextMode && c > STD_ASCII) { + | ~~^~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 297 | if ((!df_isTextMode || c <= STD_ASCII) && + | ~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 308 | if (df_isTextMode && c > STD_ASCII && + | ~~^~~~~~~~~~~ [ 80%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Built target FMCStest -[ 80%] Linking CXX executable testAbbreviations -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAbbreviations.dir/__/catch_main.cpp.o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations 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-make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 80%] Built target testAbbreviations +[ 80%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/SDMolSupplier.cpp.o 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/usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -ldl /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so -lpthread [ 80%] Linking CXX executable testFMCS cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 80%] Built target testFMCS +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 80%] Built target rdmolfiles [ 81%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so 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../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Built target RGroupDecomposition make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.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]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend.internal". -Scanning dependencies of target testRGroupDecomp Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend.internal". +Scanning dependencies of target testRGroupDecomp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' @@ -7580,8 +7613,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp +[ 81%] Built target rdFMCS +[ 81%] Linking CXX executable testAbbreviations +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAbbreviations.dir/__/catch_main.cpp.o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../../lib/libRDKitAbbreviations.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 81%] Built target testAbbreviations In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7603,299 +7643,275 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:47: -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 285 | if (df_isTextMode && c > STD_ASCII) { - | ~~^~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 297 | if ((!df_isTextMode || c <= STD_ASCII) && - | ~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 308 | if (df_isTextMode && c > STD_ASCII && - | ~~^~~~~~~~~~~ -[ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 81%] Built target rdFMCS -[ 81%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 ../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 81%] Built target testRGroupDecomp [ 81%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2020.09.4 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/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.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitFMCS.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 81%] Built target rdRGroupDecomposition cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 81%] Built target Descriptors make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= +make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend +make -f 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 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/build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= -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-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend.internal". make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend.internal". -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend -Scanning dependencies of target testAUTOCORR3D -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend.internal". -Scanning dependencies of target testCoulombMat -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend.internal". +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= -Scanning dependencies of target testEEM -Scanning dependencies of target testMORSE -make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend.internal". -Scanning dependencies of target testGETAWAY +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend.internal". -Scanning dependencies of target testAUTOCORR2D Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend.internal". -Scanning dependencies of target ChemReactions +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend.internal". +Scanning dependencies of target testAUTOCORR3D +Scanning dependencies of target testAUTOCORR2D +Scanning dependencies of target testMORSE +Scanning dependencies of target testATF +Scanning dependencies of target testCoulombMat make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target testDescriptors make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build +Scanning dependencies of target testEEM +Scanning dependencies of target testPBF +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend.internal". make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build -Scanning dependencies of target testATF +Scanning dependencies of target test3D +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend.internal". +Scanning dependencies of target testGETAWAY +make[4]: 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testCoulombMat.cpp -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake" is newer than depender 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-I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testMORSE.cpp -Scanning dependencies of target test3D make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 82%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/MDLParser.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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+make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target testRDF make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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'/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend.internal". -Dependee 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-I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testMORSE.cpp +cd 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CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testCoulombMat.cpp make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/testPBF.cpp +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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+Scanning dependencies of target ChemReactions +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend.internal". -Dependee 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+/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 285 | if (df_isTextMode && c > STD_ASCII) { + | ~~^~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 297 | if ((!df_isTextMode || c <= STD_ASCII) && + | ~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 308 | if (df_isTextMode && c > STD_ASCII && + | ~~^~~~~~~~~~~ +[ 83%] Linking CXX executable testRGroupDecomp +cd 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../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 84%] Built target testEEM +[ 83%] Built target testRGroupDecomp +[ 83%] Built target testBCUT 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-202009.4/obj-x86_64-linux-gnu' cd 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-fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 84%] Built target testCoulombMat make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend -[ 84%] Linking CXX executable testGETAWAY make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -Scanning dependencies of target testO3AAlign -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/testO3AAlign.cpp -[ 84%] Linking CXX executable testMORSE -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../lib/libRDKitDescriptors.so.1.2020.09.4 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../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 84%] Built target testGETAWAY +[ 84%] Built target testAUTOCORR3D make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend -[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu 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Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend.internal". -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 84%] Built target testMORSE +[ 84%] Built target testATF make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend -Scanning dependencies of target testMolAlign -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= +Scanning dependencies of target testMolAlign +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build +Scanning dependencies of target testO3AAlign make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend.internal". +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build [ 84%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/testMolAlign.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Scanning dependencies of target rdMolAlign +[ 84%] Linking CXX executable testRDF +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 84%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionUtils.cpp +[ 85%] Built target test3D +[ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/MoleculeParser.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7927,27 +7981,14 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:10: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:14: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. 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-I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/ReactionRunner.cpp -[ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/PreprocessRxn.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7961,101 +8002,66 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:14: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp -[ 86%] Built target testMolAlign -[ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 86%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2020.09.4 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 86%] Built target MolHash 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-202009.4/obj-x86_64-linux-gnu' -[ 86%] Linking CXX executable testWHIM cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/catch_tests.cpp +[ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp +make -f 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend.internal". +Scanning dependencies of target rdMolHash make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 86%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/catch_tests.cpp [ 86%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp +[ 86%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 86%] Built target testWHIM -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h:36, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/GraphMol.h:19, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)': -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] - 87 | x = other.x; - | ~~~~~~^ -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:88:15: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] - 88 | y = other.y; - | ~~~~~~^ -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:89:15: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] - 89 | z = other.z; - | ~~~~~~^ -[ 86%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)': -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] - 87 | x = other.x; - | ~~~~~~^ -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:88:15: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] - 88 | y = other.y; - | ~~~~~~^ -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:89:15: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] - 89 | z = other.z; - | ~~~~~~^ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 86%] Built target testO3AAlign +[ 86%] Built target testMolAlign In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8077,21 +8083,50 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 86%] Linking CXX executable testO3AAlign +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitDistGeometry.so.1.2020.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 86%] Built target rdMolHash +[ 86%] Built target testO3AAlign [ 86%] Linking CXX executable testDescriptors cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 86%] Built target testDescriptors [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2020.09.4 ../../../../lib/libRDKitForceField.so.1.2020.09.4 ../../../../lib/libRDKitOptimizer.so.1.2020.09.4 ../../../../lib/libRDKitTrajectory.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 86%] Built target testDescriptors +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 86%] Built target rdMolAlign +In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h:36, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/GraphMol.h:19, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)': +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] + 87 | x = other.x; + | ~~~~~~^ +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:88:15: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] + 88 | y = other.y; + | ~~~~~~^ +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:89:15: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] + 89 | z = other.z; + | ~~~~~~^ +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)': +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+32).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] + 87 | x = other.x; + | ~~~~~~^ +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:88:15: warning: '*((void*)(&)+32).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] + 88 | y = other.y; + | ~~~~~~^ +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:89:15: warning: '*((void*)(&)+32).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] + 89 | z = other.z; + | ~~~~~~^ +[ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 86%] Built target rdMolHash [ 87%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 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/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl @@ -8102,109 +8137,111 @@ make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= -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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend.internal". -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend.internal". -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend.internal". -Scanning dependencies of target testReaction +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend.internal". +Scanning dependencies of target Deprotect make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build Scanning dependencies of target testReactionFingerprints +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Scanning dependencies of target testEnumeration -Scanning dependencies of target rxnTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build +Scanning dependencies of target MolEnumerator +Scanning dependencies of target testReaction +Scanning dependencies of target rxnTestCatch +Scanning dependencies of target rdChemReactions +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make 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+make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.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-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend.internal". -Scanning dependencies of target rdChemReactions -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend.internal". -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build -[ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -Scanning dependencies of target MolEnumerator -Scanning dependencies of target Deprotect +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +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-202009.4/obj-x86_64-linux-gnu' +[ 87%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Deprotect.cpp [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/testReaction.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/catch_tests.cpp [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/catch_tests.cpp cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp [ 87%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp -[ 88%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp Scanning dependencies of target MolStandardize -[ 88%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 88%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Deprotect.cpp -Scanning dependencies of target MolDraw2D +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp [ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/MolEnumerator.cpp +[ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o +Scanning dependencies of target MolDraw2D make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/PositionVariation.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/LinkNode.cpp [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/MolStandardize.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.cpp [ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -[ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Metal.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/LinkNode.cpp +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8212,11 +8249,13 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202009.4/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.h:14, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:32: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -8230,34 +8269,28 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202009.4/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolPickler.h:14, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:32: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. 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-I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD 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testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Charge.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -cd 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-fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 89%] Built target testReactionFingerprints +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Normalize.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Validate.cpp [ 91%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-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 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2020.09.4 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so @@ -8275,12 +8308,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 91%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/deprotectTest.cpp -[ 91%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 91%] Built target MolEnumerator 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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --color= @@ -8292,30 +8319,43 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 91%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Fragment.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp -[ 91%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Charge.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp +[ 91%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 91%] Built target testEnumeration +[ 91%] Built target MolEnumerator make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend.internal". +[ 91%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 Scanning dependencies of target testMolEnumerator make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so [ 91%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/catch_main.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolEnumerator.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/catch_main.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 91%] Built target testEnumeration +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend.internal". +Scanning dependencies of target rdMolEnumerator +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 91%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8338,10 +8378,46 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawText.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202009.4/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:28, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ [ 91%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8363,38 +8439,140 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Fragment.cpp +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextJS.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFT.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +[ 92%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 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-DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 92%] Built target rdDeprotect +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawText.cpp -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 93%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 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/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 92%] Built target rdMolDescriptors -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend +[ 93%] Built target MolDraw2D +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend.internal". -Scanning dependencies of target rdMolEnumerator +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend.internal". +Scanning dependencies of target moldraw2DRxnTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build +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-202009.4/obj-x86_64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +[ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/rxn_test1.cpp +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS 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object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 93%] Built target molHashCatchTest +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/test1.cpp +[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp +[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/catch_tests.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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend.internal". +Scanning dependencies of target rdMolDraw2D +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend.internal". +Scanning dependencies of target rdmolops +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o +cd 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-fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolops.cpp +[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp +[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ChiralityOps.cpp +[ 94%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 94%] Built target moldraw2DRxnTest1 In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8402,25 +8580,20 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202009.4/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2D.h:28, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp:10: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolops.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 92%] Built target rdDeprotect -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8435,166 +8608,99 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp -[ 93%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/enumerator_catch.cpp -[ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +[ 94%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 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/usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 93%] Built target rdChemReactions -[ 93%] Linking CXX shared module 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../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 93%] Built target rdMolEnumerator -[ 94%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +[ 94%] Built target rdChemReactions +[ 95%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + 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, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 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.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 94%] Built target MolStandardize +[ 95%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= -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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend.internal". -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Scanning dependencies of target molValidateTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= +Scanning dependencies of target molChargeTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend.internal". -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build -Scanning dependencies of target molNormalizeTest -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Scanning dependencies of target TautomerQuery -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend.internal". Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend.internal". +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend.internal". +Scanning dependencies of target TautomerQuery +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend.internal". +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +Scanning dependencies of target molValidateTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend.internal". Scanning dependencies of target molStandardizeTest Scanning dependencies of target molFragmentTest -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend.internal". -Scanning dependencies of target molChargeTest -[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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"/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend.internal". -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testValidate.cpp -Scanning dependencies of target molStandardizeCatchTest -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build -[ 94%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -Scanning dependencies of target molTautomerTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/TautomerQuery.cpp +Scanning dependencies of target molNormalizeTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testFragment.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/test1.cpp -[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testCharge.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/catch_tests.cpp -[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testTautomer.cpp -[ 95%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 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/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o ../../../lib/libRDKitChemReactions.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 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../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so -[ 95%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../../lib/libRDKitMolHash.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 95%] Built target MolDraw2D -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend.internal". -Scanning dependencies of target molStandardizeSmallTest -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/test2.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 95%] Built target molHashCatchTest -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend.internal". -Scanning dependencies of target rdMolStandardize -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build +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-202009.4/obj-x86_64-linux-gnu' -[ 95%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp -[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Validate.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8608,134 +8714,149 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp:10: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ChiralityOps.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o +[ 96%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/test1.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/TautomerQuery.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testValidate.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testCharge.cpp /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testFragment.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testNormalize.cpp +In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp:30: +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 285 | if (df_isTextMode && c > STD_ASCII) { + | ~~^~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 297 | if ((!df_isTextMode || c <= STD_ASCII) && + | ~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] + 308 | if (df_isTextMode && c > STD_ASCII && + | ~~^~~~~~~~~~~ +[ 96%] Linking CXX executable molFragmentTest +cd 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../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 96%] Built target molChargeTest -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend +[ 96%] Built target molFragmentTest +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend.internal". -Scanning dependencies of target ScaffoldNetwork +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend.internal". +Scanning dependencies of target molTautomerTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build +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-202009.4/obj-x86_64-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Validate.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX executable molStandardizeSmallTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 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../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 97%] Linking CXX executable molNormalizeTest +[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/testTautomer.cpp +[ 96%] Linking CXX executable molNormalizeTest cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 97%] Linking CXX executable molFragmentTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -[ 97%] Linking CXX executable molValidateTest +[ 96%] Linking CXX executable molChargeTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 96%] Linking CXX executable molValidateTest cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 97%] Built target molStandardizeSmallTest -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend.internal". -Scanning dependencies of target moldraw2DRxnTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build +[ 96%] Built target molChargeTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend +[ 96%] Built target molNormalizeTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= +[ 96%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend.internal". +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +Scanning dependencies of target molStandardizeSmallTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/rxn_test1.cpp -[ 97%] Built target molNormalizeTest -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= -[ 97%] Built target molFragmentTest -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend +Scanning dependencies of target molStandardizeCatchTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend.internal". -Scanning dependencies of target moldraw2DTestCatch -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend.internal". +[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/test2.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/catch_tests.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend.internal". -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +[ 96%] Built target molValidateTest +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-202009.4/obj-x86_64-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTestCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/catch_main.cpp -Scanning dependencies of target moldraw2DTest1 +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend.internal". +Scanning dependencies of target rdMolStandardize make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +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-202009.4/obj-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/test1.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target molValidateTest -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend +[ 96%] Built target TautomerQuery +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend.internal". -Scanning dependencies of target rdMolDraw2D +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend.internal". +Scanning dependencies of target ScaffoldNetwork make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp -[ 98%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Validate.cpp +[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp +In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h:36, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:17: +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDGeom::Point2D]': +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:269:57: warning: '*((void*)(&)+32).RDGeom::Point2D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] + 269 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} + | ~~~~~~^ +/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:269:69: warning: '*((void*)(&)+32).RDGeom::Point2D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] + 269 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} + | ~~~~~~^ +[ 98%] Linking CXX executable testMolEnumerator +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/catch_main.cpp.o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target TautomerQuery -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend +[ 98%] Built target testMolEnumerator +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend.internal". -Scanning dependencies of target rdmolops +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend.internal". +Scanning dependencies of target tautomerQueryTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build +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-202009.4/obj-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolops.cpp -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Charge.cpp +[ 98%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/catch_tests.cpp +[ 98%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8749,36 +8870,17 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable moldraw2DRxnTest1 -[ 98%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 98%] Built target molStandardizeTest -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend.internal". -Scanning dependencies of target tautomerQueryTestCatch -make[4]: Leaving directory 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-DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/catch_tests.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend.internal". @@ -8792,45 +8894,6 @@ [ 98%] Linking CXX executable deprotectTest cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../../lib/libRDKitDeprotect.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target deprotectTest -[ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp -[ 98%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend.internal". -Scanning dependencies of target testScaffoldNetwork -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/catch_main.cpp -[ 98%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/catch_main.cpp.o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../../lib/libRDKitMolEnumerator.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target testMolEnumerator -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend.internal". -Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend.internal". -Scanning dependencies of target rdScaffoldNetwork -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8844,14 +8907,41 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rdmolops.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Validate.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 98%] Built target deprotectTest +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 98%] Built target moldraw2DTest1 +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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'/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 98%] Built target rxnTestCatch +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +[ 98%] Linking CXX executable molStandardizeSmallTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest 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/usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 98%] Built target molStandardizeSmallTest +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Metal.cpp +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8891,11 +8981,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ChiralityOps.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8909,14 +8994,17 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp:12: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8938,9 +9026,34 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so +[ 98%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 98%] 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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend.internal". +Scanning dependencies of target rdScaffoldNetwork +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend.internal". +Dependee "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp +Scanning dependencies of target testScaffoldNetwork +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/catch_main.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8954,31 +9067,14 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp:11: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/MolOps.cpp:30: -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::int_type boost_adaptbx::python::streambuf::overflow(boost_adaptbx::python::streambuf::int_type)': -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:285:28: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 285 | if (df_isTextMode && c > STD_ASCII) { - | ~~^~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:297:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 297 | if ((!df_isTextMode || c <= STD_ASCII) && - | ~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202009.4/Code/RDBoost/python_streambuf.h:308:30: warning: comparison of integer expressions of different signedness: 'boost_adaptbx::python::streambuf::int_type' {aka 'int'} and 'const unsigned int' [-Wsign-compare] - 308 | if (df_isTextMode && c > STD_ASCII && - | ~~^~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target rxnTestCatch -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/freetype2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/catch_tests.cpp -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8990,63 +9086,27 @@ from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/ChiralityOps.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ + from /usr/include/boost/python/object/class.hpp:9, + from /usr/include/boost/python/class.hpp:13, + 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-202009.4/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Metal.cpp -In file included from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Conformer.h:14, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.h:36, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:17: -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h: In function 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDGeom::Point2D]': -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:269:57: warning: '*((void*)(&)+32).RDGeom::Point2D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] - 269 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} - | ~~~~~~^ -/build/reproducible-path/rdkit-202009.4/Code/Geometry/point.h:269:69: warning: '*((void*)(&)+32).RDGeom::Point2D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] - 269 | Point2D(const Point2D &other) : Point(other), x(other.x), y(other.y) {} - | ~~~~~~^ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target rdTautomerQuery -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++11 -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp -[ 98%] Linking CXX executable molTautomerTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target molTautomerTest -[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o +[ 99%] Built target rdMolDraw2D +[ 99%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/build/reproducible-path/rdkit-202009.4/External -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202009.4/Code -I/build/reproducible-path/rdkit-202009.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++11 -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9060,76 +9120,46 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap.h:20, - from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: + from /build/reproducible-path/rdkit-202009.4/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - 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, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object/class.hpp:9, - from /usr/include/boost/python/class.hpp:13, - 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-202009.4/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target rdScaffoldNetwork -[ 98%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target testReaction -[ 98%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target moldraw2DTest1 -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 99%] Built target rdTautomerQuery +[ 99%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 99%] Built target rdMolDraw2D +[ 99%] Built target rdmolops [ 99%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_main.cpp.o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitCIPLabeler.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 99%] Built target moldraw2DTestCatch +[ 99%] Linking CXX executable molTautomerTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 99%] Built target molTautomerTest +[ 99%] Linking CXX executable testReaction +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so [ 99%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 99%] Built target rdMolStandardize -[ 99%] Linking CXX executable molStandardizeCatchTest -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 99%] Built target testReaction make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 99%] Built target molStandardizeCatchTest -[ 99%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitMolDraw2D.so.1.2020.09.4 ../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +[ 99%] Built target rdMolStandardize +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../../lib/libRDKitRDBoost.so.1.2020.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../../lib/libRDKitDataStructs.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libpython3.9.so /usr/lib/x86_64-linux-gnu/libboost_python39.so ../../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 99%] Built target rdmolops +[ 99%] Built target rdScaffoldNetwork [ 99%] Linking CXX executable testScaffoldNetwork cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_main.cpp.o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../../lib/libRDKitScaffoldNetwork.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl @@ -9140,6 +9170,11 @@ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../../lib/libRDKitTautomerQuery.so.1.2020.09.4 ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [100%] Built target tautomerQueryTestCatch +[100%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/rdkit-202009.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../../lib/libRDKitMolStandardize.so.1.2020.09.4 ../../../lib/libRDKitChemReactions.so.1.2020.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2020.09.4 ../../../lib/libRDKitCatalogs.so.1.2020.09.4 ../../../lib/libRDKitFingerprints.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemTransforms.so.1.2020.09.4 ../../../lib/libRDKitDescriptors.so.1.2020.09.4 ../../../lib/libRDKitFileParsers.so.1.2020.09.4 ../../../lib/libRDKitSmilesParse.so.1.2020.09.4 ../../../lib/libRDKitDepictor.so.1.2020.09.4 ../../../lib/libRDKitMolAlign.so.1.2020.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2020.09.4 ../../../lib/libRDKitAlignment.so.1.2020.09.4 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../lib/libRDKitPartialCharges.so.1.2020.09.4 ../../../lib/libRDKitSubgraphs.so.1.2020.09.4 ../../../lib/libRDKitMolTransforms.so.1.2020.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2020.09.4 ../../../lib/libRDKitGraphMol.so.1.2020.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2020.09.4 ../../../lib/libRDKitDataStructs.so.1.2020.09.4 ../../../lib/libRDKitRDGeneral.so.1.2020.09.4 -lpthread -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[100%] Built target molStandardizeCatchTest make[3]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -16951,10 +16986,10 @@ #export RDBASE=/build/reproducible-path/rdkit-202009.4 PYTHONPATH=/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu//lib:" PYTHONPATH=/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu//lib:" dh_auto_test dh_auto_test: warning: Compatibility levels before 10 are deprecated (level 9 in use) - cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=-j15 + cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=-j16 make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process -j15 +/usr/bin/ctest --force-new-ctest-process -j16 Test project /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu Start 1: testCoordGen Start 2: pyCoordGen @@ -16971,622 +17006,376 @@ Start 13: testTransforms Start 14: testGrid Start 15: geometryTestsCatch - 1/190 Test #4: testRDValue ............................ Passed 0.04 sec Start 16: testPyGeometry - 2/190 Test #6: testDataStructs ........................ Passed 0.04 sec + 1/190 Test #4: testRDValue ............................ Passed 0.04 sec Start 17: testMatrices - 3/190 Test #7: testFPB ................................ Passed 0.04 sec + 2/190 Test #6: testDataStructs ........................ Passed 0.03 sec Start 18: testConrec - 4/190 Test #13: testTransforms ......................... Passed 0.04 sec + 3/190 Test #7: testFPB ................................ Passed 0.03 sec Start 19: testAlignment - 5/190 Test #8: testMultiFPB ........................... Passed 0.06 sec + 4/190 Test #8: testMultiFPB ........................... Passed 0.03 sec Start 20: pyAlignment - 6/190 Test #15: geometryTestsCatch ..................... Passed 0.04 sec + 5/190 Test #13: testTransforms ......................... Passed 0.03 sec Start 21: testOptimizer - 7/190 Test #14: testGrid ............................... Passed 0.06 sec + 6/190 Test #15: geometryTestsCatch ..................... Passed 0.02 sec Start 22: testUFFForceField - 8/190 Test #17: testMatrices ........................... Passed 0.05 sec + 7/190 Test #17: testMatrices ........................... Passed 0.02 sec Start 23: testMMFFForceField - 9/190 Test #19: testAlignment .......................... Passed 0.04 sec + 8/190 Test #19: testAlignment .......................... Passed 0.02 sec Start 24: pyForceFieldConstraints - 10/190 Test #21: testOptimizer .......................... Passed 0.03 sec + 9/190 Test #21: testOptimizer .......................... Passed 0.01 sec Start 25: testDistGeom - 11/190 Test #18: testConrec ............................. Passed 0.08 sec + 10/190 Test #14: testGrid ............................... Passed 0.04 sec Start 26: pyDistGeom - 12/190 Test #25: testDistGeom ........................... Passed 0.04 sec + 11/190 Test #18: testConrec ............................. Passed 0.03 sec Start 27: graphmolTest1 - 13/190 Test #22: testUFFForceField ...................... Passed 0.11 sec + 12/190 Test #25: testDistGeom ........................... Passed 0.02 sec Start 28: graphmolcpTest - 14/190 Test #28: graphmolcpTest ......................... Passed 0.04 sec + 13/190 Test #28: graphmolcpTest ......................... Passed 0.03 sec Start 29: graphmolqueryTest - 15/190 Test #11: pySparseIntVect ........................ Passed 0.25 sec + 14/190 Test #29: graphmolqueryTest ...................... Passed 0.03 sec Start 30: graphmolMolOpsTest - 16/190 Test #29: graphmolqueryTest ...................... Passed 0.03 sec + 15/190 Test #22: testUFFForceField ...................... Passed 0.11 sec Start 31: graphmoltestChirality - 17/190 Test #10: pyDiscreteValueVect .................... Passed 0.33 sec + 16/190 Test #31: graphmoltestChirality .................. Passed 0.12 sec Start 32: graphmoltestPickler - 18/190 Test #2: pyCoordGen ............................. Passed 0.36 sec + 17/190 Test #11: pySparseIntVect ........................ Passed 0.29 sec Start 33: graphmoltestPicklerGlobalSetting - 19/190 Test #31: graphmoltestChirality .................. Passed 0.08 sec + 18/190 Test #33: graphmoltestPicklerGlobalSetting ....... Passed 0.02 sec Start 34: graphmolIterTest - 20/190 Test #1: testCoordGen ........................... Passed 0.38 sec + 19/190 Test #10: pyDiscreteValueVect .................... Passed 0.34 sec Start 35: hanoiTest - 21/190 Test #33: graphmoltestPicklerGlobalSetting ....... Passed 0.02 sec + 20/190 Test #12: pyFPB .................................. Passed 0.34 sec Start 36: graphmolMemTest1 - 22/190 Test #36: graphmolMemTest1 ....................... Passed 0.01 sec + 21/190 Test #1: testCoordGen ........................... Passed 0.37 sec Start 37: resMolSupplierTest - 23/190 Test #34: graphmolIterTest ....................... Passed 0.03 sec + 22/190 Test #34: graphmolIterTest ....................... Passed 0.03 sec Start 38: molBundleTest - 24/190 Test #16: testPyGeometry ......................... Passed 0.38 sec + 23/190 Test #36: graphmolMemTest1 ....................... Passed 0.02 sec Start 39: testSGroup - 25/190 Test #12: pyFPB .................................. Passed 0.41 sec + 24/190 Test #20: pyAlignment ............................ Passed 0.33 sec Start 40: test-valgrind - 26/190 Test #38: molBundleTest .......................... Passed 0.04 sec + 25/190 Test #2: pyCoordGen ............................. Passed 0.39 sec Start 41: graphmolTestsCatch - 27/190 Test #40: test-valgrind .......................... Passed 0.05 sec + 26/190 Test #38: molBundleTest .......................... Passed 0.03 sec Start 42: graphmolSGroupCatch - 28/190 Test #39: testSGroup ............................. Passed 0.08 sec + 27/190 Test #16: testPyGeometry ......................... Passed 0.38 sec Start 43: graphmolAdjustQueryCatch - 29/190 Test #41: graphmolTestsCatch ..................... Passed 0.09 sec + 28/190 Test #40: test-valgrind .......................... Passed 0.03 sec Start 44: chiralityTestsCatch - 30/190 Test #42: graphmolSGroupCatch .................... Passed 0.06 sec + 29/190 Test #39: testSGroup ............................. Passed 0.04 sec Start 45: testDepictor - 31/190 Test #26: pyDistGeom ............................. Passed 0.44 sec + 30/190 Test #26: pyDistGeom ............................. Passed 0.36 sec Start 46: pyDepictor - 32/190 Test #44: chiralityTestsCatch .................... Passed 0.06 sec + 31/190 Test #41: graphmolTestsCatch ..................... Passed 0.05 sec Start 47: smiTest1 - 33/190 Test #43: graphmolAdjustQueryCatch ............... Passed 0.10 sec + 32/190 Test #42: graphmolSGroupCatch .................... Passed 0.04 sec Start 48: smiTest2 - 34/190 Test #48: smiTest2 ............................... Passed 0.04 sec + 33/190 Test #44: chiralityTestsCatch .................... Passed 0.04 sec Start 49: cxsmilesTest - 35/190 Test #20: pyAlignment ............................ Passed 0.60 sec + 34/190 Test #48: smiTest2 ............................... Passed 0.02 sec Start 50: smaTest1 - 36/190 Test #32: graphmoltestPickler .................... Passed 0.34 sec + 35/190 Test #43: graphmolAdjustQueryCatch ............... Passed 0.06 sec Start 51: smiTestCatch - 37/190 Test #49: cxsmilesTest ........................... Passed 0.06 sec + 36/190 Test #49: cxsmilesTest ........................... Passed 0.03 sec Start 52: fileParsersTest1 - 38/190 Test #51: smiTestCatch ........................... Passed 0.05 sec + 37/190 Test #51: smiTestCatch ........................... Passed 0.04 sec Start 53: testMolSupplier - 39/190 Test #50: smaTest1 ............................... Passed 0.19 sec + 38/190 Test #32: graphmoltestPickler .................... Passed 0.27 sec Start 54: testGeneralFileReader - 40/190 Test #47: smiTest1 ............................... Passed 0.28 sec + 39/190 Test #50: smaTest1 ............................... Passed 0.17 sec Start 55: testMultithreadedMolSupplier - 41/190 Test #45: testDepictor ........................... Passed 0.34 sec + 40/190 Test #47: smiTest1 ............................... Passed 0.21 sec Start 56: testMolWriter - 42/190 Test #9: pyBV ................................... Passed 0.94 sec + 41/190 Test #54: testGeneralFileReader .................. Passed 0.13 sec Start 57: testTplParser - 43/190 Test #57: testTplParser .......................... Passed 0.04 sec + 42/190 Test #57: testTplParser .......................... Passed 0.04 sec Start 58: testMol2ToMol - 44/190 Test #58: testMol2ToMol .......................... Passed 0.04 sec + 43/190 Test #45: testDepictor ........................... Passed 0.33 sec Start 59: testSequence - 45/190 Test #53: testMolSupplier ........................ Passed 0.33 sec + 44/190 Test #58: testMol2ToMol .......................... Passed 0.04 sec Start 60: testExtendedStereoParsing - 46/190 Test #54: testGeneralFileReader .................. Passed 0.23 sec + 45/190 Test #53: testMolSupplier ........................ Passed 0.30 sec Start 61: fileParsersCatchTest - 47/190 Test #59: testSequence ........................... Passed 0.07 sec + 46/190 Test #59: testSequence ........................... Passed 0.06 sec Start 62: testPropertyLists - 48/190 Test #60: testExtendedStereoParsing .............. Passed 0.05 sec + 47/190 Test #60: testExtendedStereoParsing .............. Passed 0.05 sec Start 63: testSubstructMatch - 49/190 Test #62: testPropertyLists ...................... Passed 0.05 sec + 48/190 Test #62: testPropertyLists ...................... Passed 0.04 sec Start 64: substructTestCatch - 50/190 Test #61: fileParsersCatchTest ................... Passed 0.10 sec + 49/190 Test #61: fileParsersCatchTest ................... Passed 0.07 sec Start 65: testReaction - 51/190 Test #30: graphmolMolOpsTest ..................... Passed 0.94 sec + 50/190 Test #64: substructTestCatch ..................... Passed 0.04 sec Start 66: testReactionFingerprints - 52/190 Test #64: substructTestCatch ..................... Passed 0.05 sec + 51/190 Test #56: testMolWriter .......................... Passed 0.31 sec Start 67: testEnumeration - 53/190 Test #56: testMolWriter .......................... Passed 0.33 sec + 52/190 Test #66: testReactionFingerprints ............... Passed 0.08 sec Start 68: rxnTestCatch - 54/190 Test #46: pyDepictor ............................. Passed 0.66 sec + 53/190 Test #46: pyDepictor ............................. Passed 0.62 sec Start 69: pyChemReactions - 55/190 Test #66: testReactionFingerprints ............... Passed 0.05 sec + 54/190 Test #24: pyForceFieldConstraints ................ Passed 0.99 sec Start 70: pyChemReactionEnumerations - 56/190 Test #24: pyForceFieldConstraints ................ Passed 1.18 sec + 55/190 Test #68: rxnTestCatch ........................... Passed 0.15 sec Start 71: pyChemReactionSanitize - 57/190 Test #68: rxnTestCatch ........................... Passed 0.10 sec + 56/190 Test #9: pyBV ................................... Passed 1.18 sec Start 72: testChemTransforms - 58/190 Test #3: testDict ............................... Passed 1.37 sec + 57/190 Test #63: testSubstructMatch ..................... Passed 0.46 sec Start 73: chemTransformsTestCatch - 59/190 Test #72: testChemTransforms ..................... Passed 0.10 sec + 58/190 Test #72: testChemTransforms ..................... Passed 0.11 sec Start 74: tautomerQueryTestCatch - 60/190 Test #73: chemTransformsTestCatch ................ Passed 0.07 sec + 59/190 Test #73: chemTransformsTestCatch ................ Passed 0.06 sec Start 75: pyTautomerQuery - 61/190 Test #65: testReaction ........................... Passed 0.40 sec + 60/190 Test #30: graphmolMolOpsTest ..................... Passed 1.23 sec Start 76: testSubgraphs1 - 62/190 Test #63: testSubstructMatch ..................... Passed 0.49 sec + 61/190 Test #65: testReaction ........................... Passed 0.52 sec Start 77: testSubgraphs2 - 63/190 Test #74: tautomerQueryTestCatch ................. Passed 0.20 sec + 62/190 Test #77: testSubgraphs2 ......................... Passed 0.03 sec Start 78: filterCatalogTest - 64/190 Test #77: testSubgraphs2 ......................... Passed 0.04 sec + 63/190 Test #74: tautomerQueryTestCatch ................. Passed 0.15 sec Start 79: pyFilterCatalog - 65/190 Test #71: pyChemReactionSanitize ................. Passed 0.48 sec + 64/190 Test #71: pyChemReactionSanitize ................. Passed 0.43 sec Start 80: testFragCatalog - 66/190 Test #69: pyChemReactions ........................ Passed 0.55 sec + 65/190 Test #78: filterCatalogTest ...................... Passed 0.25 sec Start 81: pyFragCatalog - 67/190 Test #75: pyTautomerQuery ........................ Passed 0.42 sec + 66/190 Test #69: pyChemReactions ........................ Passed 0.67 sec Start 82: testDescriptors - 68/190 Test #78: filterCatalogTest ...................... Passed 0.33 sec + 67/190 Test #3: testDict ............................... Passed 1.73 sec Start 83: testAUTOCORR2D - 69/190 Test #76: testSubgraphs1 ......................... Passed 0.38 sec + 68/190 Test #75: pyTautomerQuery ........................ Passed 0.40 sec Start 84: testATF - 70/190 Test #84: testATF ................................ Passed 0.03 sec + 69/190 Test #84: testATF ................................ Passed 0.03 sec Start 85: testBCUT - 71/190 Test #81: pyFragCatalog .......................... Passed 0.63 sec + 70/190 Test #76: testSubgraphs1 ......................... Passed 0.40 sec Start 86: testEEM - 72/190 Test #80: testFragCatalog ........................ Passed 0.70 sec + 71/190 Test #81: pyFragCatalog .......................... Passed 0.41 sec Start 87: testPBF - 73/190 Test #87: testPBF ................................ Passed 0.21 sec + 72/190 Test #83: testAUTOCORR2D ......................... Passed 0.40 sec Start 88: testRDFcustom - 74/190 Test #83: testAUTOCORR2D ......................... Passed 0.77 sec + 73/190 Test #80: testFragCatalog ........................ Passed 0.79 sec Start 89: testRDF - 75/190 Test #86: testEEM ................................ Passed 1.09 sec + 74/190 Test #87: testPBF ................................ Passed 0.26 sec Start 90: testMORSE - 76/190 Test #85: testBCUT ............................... Passed 1.67 sec + 75/190 Test #86: testEEM ................................ Passed 0.77 sec Start 91: test3D - 77/190 Test #37: resMolSupplierTest ..................... Passed 3.62 sec + 76/190 Test #85: testBCUT ............................... Passed 0.80 sec Start 92: testWHIM - 78/190 Test #70: pyChemReactionEnumerations ............. Passed 2.92 sec + 77/190 Test #70: pyChemReactionEnumerations ............. Passed 1.77 sec Start 93: testGETAWAY - 79/190 Test #79: pyFilterCatalog ........................ Passed 2.55 sec + 78/190 Test #92: testWHIM ............................... Passed 0.42 sec Start 94: testAUTOCORR3D - 80/190 Test #92: testWHIM ............................... Passed 0.32 sec + 79/190 Test #91: test3D ................................. Passed 0.51 sec Start 95: testCoulombMat - 81/190 Test #95: testCoulombMat ......................... Passed 0.03 sec + 80/190 Test #95: testCoulombMat ......................... Passed 0.09 sec Start 96: pyMolDescriptors - 82/190 Test #91: test3D ................................. Passed 1.04 sec + 81/190 Test #79: pyFilterCatalog ........................ Passed 1.89 sec Start 97: pyMolDescriptors3D - 83/190 Test #96: pyMolDescriptors ....................... Passed 0.43 sec + 82/190 Test #94: testAUTOCORR3D ......................... Passed 0.44 sec Start 98: testFingerprints - 84/190 Test #94: testAUTOCORR3D ......................... Passed 0.80 sec + 83/190 Test #90: testMORSE .............................. Passed 1.13 sec Start 99: testMHFPFingerprint - 85/190 Test #99: testMHFPFingerprint .................... Passed 0.12 sec + 84/190 Test #99: testMHFPFingerprint .................... Passed 0.14 sec Start 100: testFingerprintGenerators - 86/190 Test #35: hanoiTest .............................. Passed 4.95 sec + 85/190 Test #89: testRDF ................................ Passed 1.82 sec Start 101: fpTestCatch - 87/190 Test #101: fpTestCatch ............................ Passed 0.08 sec + 86/190 Test #96: pyMolDescriptors ....................... Passed 1.05 sec Start 102: pyTestGenerator - 88/190 Test #89: testRDF ................................ Passed 2.71 sec + 87/190 Test #97: pyMolDescriptors3D ..................... Passed 0.86 sec Start 103: pyTestMHFP - 89/190 Test #90: testMORSE .............................. Passed 2.17 sec + 88/190 Test #35: hanoiTest .............................. Passed 3.86 sec Start 104: testPartialCharges - 90/190 Test #104: testPartialCharges ..................... Passed 0.07 sec + 89/190 Test #101: fpTestCatch ............................ Passed 0.07 sec Start 105: pyPartialCharges - 91/190 Test #100: testFingerprintGenerators .............. Passed 0.87 sec + 90/190 Test #104: testPartialCharges ..................... Passed 0.05 sec Start 106: testMolTransforms - 92/190 Test #97: pyMolDescriptors3D ..................... Passed 1.31 sec + 91/190 Test #106: testMolTransforms ...................... Passed 0.08 sec Start 107: pyMolTransforms - 93/190 Test #106: testMolTransforms ...................... Passed 0.07 sec + 92/190 Test #103: pyTestMHFP ............................. Passed 0.37 sec Start 108: testMMFFForceFieldHelpers - 94/190 Test #103: pyTestMHFP ............................. Passed 0.67 sec + 93/190 Test #102: pyTestGenerator ........................ Passed 0.51 sec Start 109: testMMFFForceFieldHelpersMultiThread - 95/190 Test #102: pyTestGenerator ........................ Passed 0.76 sec + 94/190 Test #105: pyPartialCharges ....................... Passed 0.50 sec Start 110: testUFFForceFieldHelpers - 96/190 Test #82: testDescriptors ........................ Passed 4.70 sec + 95/190 Test #37: resMolSupplierTest ..................... Passed 4.40 sec Start 111: testCrystalForceField - 97/190 Test #107: pyMolTransforms ........................ Passed 0.62 sec + 96/190 Test #107: pyMolTransforms ........................ Passed 0.49 sec Start 112: pyForceFieldHelpers - 98/190 Test #109: testMMFFForceFieldHelpersMultiThread ... Passed 0.60 sec + 97/190 Test #111: testCrystalForceField .................. Passed 0.24 sec Start 113: testDistGeomHelpers - 99/190 Test #105: pyPartialCharges ....................... Passed 0.99 sec + 98/190 Test #100: testFingerprintGenerators .............. Passed 1.47 sec Start 114: pyDistGeomHelpers -100/190 Test #111: testCrystalForceField .................. Passed 0.30 sec + 99/190 Test #109: testMMFFForceFieldHelpersMultiThread ... Passed 0.46 sec Start 115: testMolAlign -101/190 Test #115: testMolAlign ........................... Passed 0.30 sec +100/190 Test #112: pyForceFieldHelpers .................... Passed 0.53 sec Start 116: testO3AAlign -102/190 Test #112: pyForceFieldHelpers .................... Passed 0.83 sec +101/190 Test #115: testMolAlign ........................... Passed 0.30 sec Start 117: pyMolAlign -103/190 Test #55: testMultithreadedMolSupplier ........... Passed 7.85 sec +102/190 Test #82: testDescriptors ........................ Passed 3.99 sec Start 118: testFeatures -104/190 Test #118: testFeatures ........................... Passed 0.06 sec +103/190 Test #118: testFeatures ........................... Passed 0.07 sec Start 119: pyChemicalFeatures -105/190 Test #93: testGETAWAY ............................ Passed 4.87 sec +104/190 Test #119: pyChemicalFeatures ..................... Passed 0.88 sec Start 120: testShapeHelpers -106/190 Test #120: testShapeHelpers ....................... Passed 0.08 sec +105/190 Test #120: testShapeHelpers ....................... Passed 0.06 sec Start 121: pyShapeHelpers -107/190 Test #88: testRDFcustom .......................... Passed 6.54 sec +106/190 Test #93: testGETAWAY ............................ Passed 3.93 sec Start 122: testMolCatalog -108/190 Test #122: testMolCatalog ......................... Passed 0.03 sec +107/190 Test #122: testMolCatalog ......................... Passed 0.04 sec Start 123: pyMolCatalog -109/190 Test #119: pyChemicalFeatures ..................... Passed 0.50 sec +108/190 Test #123: pyMolCatalog ........................... Passed 0.52 sec Start 124: moldraw2DTest1 -110/190 Test #121: pyShapeHelpers ......................... Passed 1.01 sec +109/190 Test #121: pyShapeHelpers ......................... Passed 0.63 sec Start 125: moldraw2DTestCatch -111/190 Test #123: pyMolCatalog ........................... Passed 1.01 sec +110/190 Test #125: moldraw2DTestCatch ..................... Passed 0.19 sec Start 126: moldraw2DRxnTest1 -112/190 Test #125: moldraw2DTestCatch ..................... Passed 0.27 sec +111/190 Test #126: moldraw2DRxnTest1 ...................... Passed 0.29 sec Start 127: pyMolDraw2D -113/190 Test #126: moldraw2DRxnTest1 ...................... Passed 0.28 sec +112/190 Test #127: pyMolDraw2D ............................ Passed 1.39 sec Start 128: testFMCS -114/190 Test #108: testMMFFForceFieldHelpers .............. Passed 5.82 sec +113/190 Test #108: testMMFFForceFieldHelpers .............. Passed 5.47 sec Start 129: pyFMCS -115/190 Test #127: pyMolDraw2D ............................ Passed 1.65 sec +114/190 Test #88: testRDFcustom .......................... Passed 8.76 sec Start 130: FMCStest -116/190 Test #130: FMCStest ............................... Passed 0.04 sec +115/190 Test #130: FMCStest ............................... Passed 0.03 sec Start 131: molHashCatchTest -117/190 Test #131: molHashCatchTest ....................... Passed 0.03 sec +116/190 Test #131: molHashCatchTest ....................... Passed 0.03 sec Start 132: pyMolHash -118/190 Test #110: testUFFForceFieldHelpers ............... Passed 6.04 sec +117/190 Test #110: testUFFForceFieldHelpers ............... Passed 6.38 sec Start 133: testMMPA -119/190 Test #98: testFingerprints ....................... Passed 7.45 sec +118/190 Test #55: testMultithreadedMolSupplier ........... Passed 10.64 sec Start 134: pyMMPA -120/190 Test #133: testMMPA ............................... Passed 0.25 sec +119/190 Test #132: pyMolHash .............................. Passed 0.36 sec Start 135: testCIPLabeler -121/190 Test #135: testCIPLabeler ......................... Passed 0.06 sec +120/190 Test #133: testMMPA ............................... Passed 0.27 sec Start 136: pyCIPLabelsWrapTest -122/190 Test #132: pyMolHash .............................. Passed 0.52 sec +121/190 Test #135: testCIPLabeler ......................... Passed 0.08 sec Start 137: pyCIPLabelsValidation -123/190 Test #136: pyCIPLabelsWrapTest .................... Passed 0.57 sec +122/190 Test #98: testFingerprints ....................... Passed 8.17 sec Start 138: deprotectTest -124/190 Test #138: deprotectTest .......................... Passed 0.11 sec +123/190 Test #138: deprotectTest .......................... Passed 0.14 sec Start 139: pyDeprotect -125/190 Test #128: testFMCS ............................... Passed 3.22 sec +124/190 Test #136: pyCIPLabelsWrapTest .................... Passed 0.52 sec Start 140: testReducedGraphs -126/190 Test #140: testReducedGraphs ...................... Passed 0.04 sec +125/190 Test #140: testReducedGraphs ...................... Passed 0.10 sec Start 141: pyReducedGraphs -127/190 Test #139: pyDeprotect ............................ Passed 0.64 sec +126/190 Test #52: fileParsersTest1 ....................... Passed 11.86 sec Start 142: trajectoryTest -128/190 Test #141: pyReducedGraphs ........................ Passed 0.42 sec +127/190 Test #139: pyDeprotect ............................ Passed 0.76 sec Start 143: substructLibraryTest -129/190 Test #134: pyMMPA ................................. Passed 2.22 sec +128/190 Test #141: pyReducedGraphs ........................ Passed 0.71 sec Start 144: pySubstructLibrary -130/190 Test #142: trajectoryTest ......................... Passed 0.82 sec +129/190 Test #142: trajectoryTest ......................... Passed 0.40 sec Start 145: testRGroupDecomp -131/190 Test #52: fileParsersTest1 ....................... Passed 14.97 sec +130/190 Test #134: pyMMPA ................................. Passed 2.15 sec Start 146: pyRGroupDecomposition -132/190 Test #124: moldraw2DTest1 ......................... Passed 8.31 sec +131/190 Test #128: testFMCS ............................... Passed 4.36 sec Start 147: molInterchangeTest1 -133/190 Test #143: substructLibraryTest ................... Passed 3.40 sec +132/190 Test #147: molInterchangeTest1 .................... Passed 0.04 sec Start 148: pyMolInterchange -134/190 Test #147: molInterchangeTest1 .................... Passed 0.08 sec +133/190 Test #67: testEnumeration ........................ Passed 13.21 sec Start 149: testSLNParse -135/190 Test #149: testSLNParse ........................... Passed 0.09 sec +134/190 Test #149: testSLNParse ........................... Passed 0.05 sec Start 150: pySLNParse -136/190 Test #148: pyMolInterchange ....................... Passed 0.35 sec +135/190 Test #148: pyMolInterchange ....................... Passed 0.69 sec Start 151: pyGraphMolWrap -137/190 Test #67: testEnumeration ........................ Passed 16.90 sec +136/190 Test #124: moldraw2DTest1 ......................... Passed 7.31 sec Start 152: pyTestConformerWrap -138/190 Test #152: pyTestConformerWrap .................... Passed 0.48 sec +137/190 Test #152: pyTestConformerWrap .................... Passed 0.40 sec Start 153: pyTestTrajectory -139/190 Test #150: pySLNParse ............................. Passed 0.85 sec +138/190 Test #150: pySLNParse ............................. Passed 0.82 sec Start 154: pyTestSGroups -140/190 Test #154: pyTestSGroups .......................... Passed 0.75 sec +139/190 Test #143: substructLibraryTest ................... Passed 3.11 sec Start 155: pyTestThreads -141/190 Test #153: pyTestTrajectory ....................... Passed 0.89 sec +140/190 Test #154: pyTestSGroups .......................... Passed 0.74 sec Start 156: pyTestMultithreadedMolSupplier -142/190 Test #129: pyFMCS ................................. Passed 8.45 sec +141/190 Test #153: pyTestTrajectory ....................... Passed 0.79 sec Start 157: pyTestPropertyLists -143/190 Test #156: pyTestMultithreadedMolSupplier ......... Passed 1.02 sec +142/190 Test #129: pyFMCS ................................. Passed 5.82 sec Start 158: molStandardizeTest -144/190 Test #146: pyRGroupDecomposition .................. Passed 5.26 sec +143/190 Test #157: pyTestPropertyLists .................... Passed 0.47 sec Start 159: molNormalizeTest -145/190 Test #157: pyTestPropertyLists .................... Passed 0.75 sec +144/190 Test #156: pyTestMultithreadedMolSupplier ......... Passed 0.66 sec Start 160: molValidateTest -146/190 Test #159: molNormalizeTest ....................... Passed 0.23 sec +145/190 Test #160: molValidateTest ........................ Passed 0.10 sec Start 161: molChargeTest -147/190 Test #160: molValidateTest ........................ Passed 0.15 sec +146/190 Test #159: molNormalizeTest ....................... Passed 0.27 sec Start 162: molTautomerTest -148/190 Test #161: molChargeTest .......................... Passed 0.14 sec +147/190 Test #161: molChargeTest .......................... Passed 0.20 sec Start 163: molStandardizeSmallTest -149/190 Test #163: molStandardizeSmallTest ................ Passed 0.12 sec +148/190 Test #163: molStandardizeSmallTest ................ Passed 0.05 sec Start 164: molFragmentTest -150/190 Test #164: molFragmentTest ........................ Passed 0.11 sec +149/190 Test #164: molFragmentTest ........................ Passed 0.12 sec Start 165: molStandardizeCatchTest -151/190 Test #165: molStandardizeCatchTest ................ Passed 0.17 sec +150/190 Test #158: molStandardizeTest ..................... Passed 1.19 sec Start 166: pyMolStandardize -152/190 Test #158: molStandardizeTest ..................... Passed 1.74 sec +151/190 Test #165: molStandardizeCatchTest ................ Passed 0.19 sec Start 167: testScaffoldNetwork -153/190 Test #137: pyCIPLabelsValidation .................. Passed 9.86 sec +152/190 Test #146: pyRGroupDecomposition .................. Passed 4.79 sec Start 168: pyScaffoldNetwork -154/190 Test #145: testRGroupDecomp ....................... Passed 7.87 sec +153/190 Test #168: pyScaffoldNetwork ...................... Passed 0.70 sec Start 169: pyScaffoldNetworkPickling -155/190 Test #169: pyScaffoldNetworkPickling .............. Passed 0.40 sec +154/190 Test #145: testRGroupDecomp ....................... Passed 6.40 sec Start 170: testMolEnumerator -156/190 Test #168: pyScaffoldNetwork ...................... Passed 0.46 sec +155/190 Test #167: testScaffoldNetwork .................... Passed 2.06 sec Start 171: pyMolEnumerator -157/190 Test #170: testMolEnumerator ...................... Passed 0.05 sec +156/190 Test #170: testMolEnumerator ...................... Passed 0.05 sec Start 172: testAbbreviations -158/190 Test #23: testMMFFForceField ..................... Passed 22.95 sec +157/190 Test #137: pyCIPLabelsValidation .................. Passed 7.85 sec Start 173: pyAbbreviations -159/190 Test #172: testAbbreviations ...................... Passed 0.06 sec +158/190 Test #172: testAbbreviations ...................... Passed 0.05 sec Start 174: testQuery -160/190 Test #174: testQuery .............................. Passed 0.03 sec +159/190 Test #169: pyScaffoldNetworkPickling .............. Passed 0.35 sec Start 175: testMatCalc -161/190 Test #175: testMatCalc ............................ Passed 0.02 sec +160/190 Test #174: testQuery .............................. Passed 0.01 sec Start 176: pyMatCalc -162/190 Test #171: pyMolEnumerator ........................ Passed 0.40 sec +161/190 Test #175: testMatCalc ............................ Passed 0.01 sec Start 177: testSimDivPickers -163/190 Test #177: testSimDivPickers ...................... Passed 0.01 sec +162/190 Test #177: testSimDivPickers ...................... Passed 0.01 sec Start 178: pickersTestsCatch -164/190 Test #173: pyAbbreviations ........................ Passed 0.39 sec +163/190 Test #178: pickersTestsCatch ...................... Passed 0.11 sec Start 179: pySimDivPickers -165/190 Test #167: testScaffoldNetwork .................... Passed 1.23 sec +164/190 Test #173: pyAbbreviations ........................ Passed 0.38 sec Start 180: pyRanker -166/190 Test #178: pickersTestsCatch ...................... Passed 0.13 sec +165/190 Test #171: pyMolEnumerator ........................ Passed 0.48 sec Start 181: testChemicalFeatures -167/190 Test #181: testChemicalFeatures ................... Passed 0.02 sec +166/190 Test #181: testChemicalFeatures ................... Passed 0.01 sec Start 182: pyFeatures -168/190 Test #180: pyRanker ............................... Passed 0.33 sec +167/190 Test #166: pyMolStandardize ....................... Passed 2.68 sec Start 183: pythonTestDbCLI -169/190 Test #182: pyFeatures ............................. Passed 0.42 sec +168/190 Test #180: pyRanker ............................... Passed 0.31 sec Start 184: pythonTestDirML -170/190 Test #176: pyMatCalc .............................. Passed 1.03 sec +169/190 Test #182: pyFeatures ............................. Passed 0.39 sec Start 185: pythonTestDirDataStructs -171/190 Test #166: pyMolStandardize ....................... Passed 2.45 sec +170/190 Test #176: pyMatCalc .............................. Passed 0.85 sec Start 186: pythonTestDirDbase -172/190 Test #162: molTautomerTest ........................ Passed 3.39 sec +171/190 Test #155: pyTestThreads .......................... Passed 4.54 sec Start 187: pythonTestDirSimDivFilters -173/190 Test #186: pythonTestDirDbase ..................... Passed 1.00 sec +172/190 Test #162: molTautomerTest ........................ Passed 3.80 sec Start 188: pythonTestDirVLib -174/190 Test #187: pythonTestDirSimDivFilters ............. Passed 0.69 sec +173/190 Test #187: pythonTestDirSimDivFilters ............. Passed 0.51 sec Start 189: pythonTestDirChem -175/190 Test #185: pythonTestDirDataStructs ............... Passed 1.44 sec +174/190 Test #186: pythonTestDirDbase ..................... Passed 0.74 sec Start 190: pythonTestSping -176/190 Test #179: pySimDivPickers ........................ Passed 2.50 sec -177/190 Test #188: pythonTestDirVLib ...................... Passed 0.94 sec -178/190 Test #190: pythonTestSping ........................ Passed 0.99 sec -179/190 Test #117: pyMolAlign ............................. Passed 19.29 sec -180/190 Test #155: pyTestThreads .......................... Passed 7.61 sec -181/190 Test #144: pySubstructLibrary ..................... Passed 15.97 sec -182/190 Test #151: pyGraphMolWrap .........................***Failed 15.17 sec -..............[08:06:05] SMARTS Parse Error: syntax error while parsing: fiib -[08:06:05] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -....[08:06:05] ERROR: Problems encountered parsing data fields -[08:06:05] ERROR: moving to the beginning of the next molecule -[08:06:05] ERROR: Problems encountered parsing data fields -[08:06:05] ERROR: moving to the beginning of the next molecule -[08:06:05] Spurious data before the first property will be ignored -[08:06:05] Property will be truncated after the first blank line -[08:06:05] Property will be truncated after the first blank line -[08:06:05] Property will be truncated after the first blank line -[08:06:05] ERROR: Problems encountered parsing data fields -[08:06:05] ERROR: moving to the beginning of the next molecule -[08:06:05] ERROR: Problems encountered parsing data fields -[08:06:05] ERROR: moving to the beginning of the next molecule -[08:06:05] Spurious data before the first property will be ignored -[08:06:05] Property will be truncated after the first blank line -[08:06:05] Property will be truncated after the first blank line -[08:06:05] Property will be truncated after the first blank line -[08:06:05] ERROR: Problems encountered parsing data fields -[08:06:05] ERROR: moving to the beginning of the next molecule -[08:06:05] Property will be truncated after the first blank line -[08:06:05] ERROR: Problems encountered parsing data fields -[08:06:05] ERROR: moving to the beginning of the next molecule -[08:06:05] Property will be truncated after the first blank line -.[08:06:05] SMILES Parse Error: syntax error while parsing: fail -[08:06:05] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -[08:06:05] ERROR: Smiles parse error on line 2 -[08:06:05] ERROR: Cannot create molecule from : 'fail' ->>> This may result in an infinite loop. It should finish almost instantly -<<< OK, it finished. -............[08:06:05] Explicit valence for atom # 1 C, 5, is greater than permitted -........../build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rough_test.py:2100: DeprecationWarning: Please use assertEqual instead. - self.assertEquals(ri.NumRings(), 2) -..[08:06:05] non-ring atom 0 marked aromatic -[08:06:05] non-ring atom 0 marked aromatic -[08:06:05] - -**** -Range Error -idx -Violation occurred on line 183 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.cpp -Failed Expression: 12 < 6 -**** - -[08:06:05] non-ring atom 0 marked aromatic -[08:06:05] non-ring atom 0 marked aromatic -[08:06:05] - -**** -Range Error -idx -Violation occurred on line 183 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.cpp -Failed Expression: 12 < 6 -**** - -...............[08:06:05] 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. -[08:06:05] 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. -..............[08:06:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 - -[08:06:05] Explicit valence for atom # 1 C, 5, is greater than permitted -...............................................F.[08:06:13] Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:13] Explicit valence for atom # 6 F, 2, is greater than permitted -[08:06:13] Can't kekulize mol. Unkekulized atoms: 3 4 5 - -..............[08:06:19] - -**** -Pre-condition Violation -no owner -Violation occurred on line 128 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.h -Failed Expression: dp_mol -**** - -[08:06:19] - -**** -Pre-condition Violation -no owner -Violation occurred on line 128 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.h -Failed Expression: dp_mol -**** - -[08:06:19] - -**** -Pre-condition Violation -no owner -Violation occurred on line 128 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.h -Failed Expression: dp_mol -**** - -[08:06:19] - -**** -Pre-condition Violation -no owner -Violation occurred on line 128 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.h -Failed Expression: dp_mol -**** - -[08:06:19] - -**** -Pre-condition Violation -no owner -Violation occurred on line 128 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Atom.h -Failed Expression: dp_mol -**** - -.....[08:06:19] - -**** -Range Error -atomIdx1 -Violation occurred on line 298 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RWMol.cpp -Failed Expression: 0 < 0 -**** - -....[08:06:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -..[08:06:19] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -[08:06:19] ERROR: Smiles parse error on line 0 -[08:06:19] ERROR: Cannot create molecule from : 'c1ccccc' -[08:06:19] SMILES Parse Error: extra open parentheses for input: 'C(C' -[08:06:19] ERROR: Smiles parse error on line 3 -[08:06:19] ERROR: Cannot create molecule from : 'C(C' -[08:06:19] Explicit valence for atom # 1 C, 5, is greater than permitted -[08:06:19] ERROR: Could not sanitize molecule on line 6 -[08:06:19] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -[08:06:19] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -[08:06:19] ERROR: Smiles parse error on line 0 -[08:06:19] ERROR: Cannot create molecule from : 'c1ccccc' -[08:06:19] SMILES Parse Error: extra open parentheses for input: 'C(C' -[08:06:19] ERROR: Smiles parse error on line 3 -[08:06:19] ERROR: Cannot create molecule from : 'C(C' -[08:06:19] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -[08:06:19] ERROR: Smiles parse error on line 6 -[08:06:19] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -[08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] ERROR: Could not sanitize molecule ending on line 21 -[08:06:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] ERROR: EOF hit while reading atoms -[08:06:19] ERROR: moving to the beginning of the next molecule -[08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] ERROR: Could not sanitize molecule ending on line 21 -[08:06:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] ERROR: EOF hit while reading atoms -[08:06:19] ERROR: moving to the beginning of the next molecule -.......[08:06:19] - -**** -Range Error -idx -Violation occurred on line 183 in file /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ROMol.cpp -Failed Expression: 3 < 1 -**** - -..[08:06:19] 1 -[08:06:19] 2 -[08:06:19] 1 -[08:06:19] 2 -....................[08:06:19] WARNING: not removing hydrogen atom without neighbors -RDKit WARNING: [08:06:19] WARNING: not removing hydrogen atom without neighbors -[08:06:19] WARNING: not removing hydrogen atom with dummy atom neighbors -RDKit WARNING: [08:06:19] WARNING: not removing hydrogen atom with dummy atom neighbors -[08:06:19] WARNING: not removing hydrogen atom with wedged bond -RDKit WARNING: [08:06:19] WARNING: not removing hydrogen atom with wedged bond -[08:06:19] WARNING: not removing hydrogen atom without neighbors -RDKit WARNING: [08:06:19] WARNING: not removing hydrogen atom without neighbors -[08:06:19] WARNING: not removing hydrogen atom with dummy atom neighbors -RDKit WARNING: [08:06:19] WARNING: not removing hydrogen atom with dummy atom neighbors -.....[08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -RDKit ERROR: [08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 - -RDKit ERROR: [08:06:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -RDKit ERROR: -.[08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -RDKit ERROR: [08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -RDKit ERROR: [08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -RDKit ERROR: [08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -RDKit ERROR: [08:06:19] Explicit valence for atom # 1 F, 2, is greater than permitted -[08:06:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 - -RDKit ERROR: [08:06:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -RDKit ERROR: -[08:06:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 - -RDKit ERROR: [08:06:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -RDKit ERROR: -[08:06:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 - -RDKit ERROR: [08:06:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -RDKit ERROR: -.........[08:06:20] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -RDKit ERROR: [08:06:20] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -[08:06:20] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -RDKit ERROR: [08:06:20] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -..[08:06:20] SMILES Parse Error: syntax error while parsing: error -RDKit ERROR: [08:06:20] SMILES Parse Error: syntax error while parsing: error -[08:06:20] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -RDKit ERROR: [08:06:20] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -[08:06:20] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -RDKit ERROR: [08:06:20] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -[08:06:20] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -RDKit ERROR: [08:06:20] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -[08:06:20] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -RDKit ERROR: [08:06:20] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -............... -====================================================================== -FAIL: testCrambin (__main__.TestCase) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap/rough_test.py", line 4012, in testCrambin - self.assertEqual(matches, ((166, 167, 168), (298, 299, 300), (320, 321, 326))) -AssertionError: Tuples differ: ((166, 167, 168), (298, 299, 300), (320, 326, 321)) != ((166, 167, 168), (298, 299, 300), (320, 321, 326)) - -First differing element 2: -(320, 326, 321) -(320, 321, 326) - -- ((166, 167, 168), (298, 299, 300), (320, 326, 321)) -? ----- - -+ ((166, 167, 168), (298, 299, 300), (320, 321, 326)) -? +++++ - - ----------------------------------------------------------------------- -Ran 207 tests in 14.454s - -FAILED (failures=1) -643 -supplier: -supplier: -supplier: - -183/190 Test #114: pyDistGeomHelpers ...................... Passed 30.72 sec -184/190 Test #184: pythonTestDirML ........................ Passed 18.05 sec -185/190 Test #183: pythonTestDbCLI ........................ Passed 25.40 sec -186/190 Test #116: testO3AAlign ........................... Passed 42.97 sec -187/190 Test #27: graphmolTest1 .......................... Passed 56.85 sec -188/190 Test #113: testDistGeomHelpers .................... Passed 58.54 sec -189/190 Test #5: testConcurrentQueue .................... Passed 72.35 sec -190/190 Test #189: pythonTestDirChem ...................... Passed 133.94 sec - -99% tests passed, 1 tests failed out of 190 - -Total Test time (real) = 159.28 sec - -The following tests FAILED: - 151 - pyGraphMolWrap (Failed) -Errors while running CTest -make[2]: *** [Makefile:129: test] Error 8 +175/190 Test #188: pythonTestDirVLib ...................... Passed 0.83 sec +176/190 Test #185: pythonTestDirDataStructs ............... Passed 1.47 sec +177/190 Test #179: pySimDivPickers ........................ Passed 2.24 sec +178/190 Test #190: pythonTestSping ........................ Passed 0.98 sec +179/190 Test #23: testMMFFForceField ..................... Passed 22.77 sec +180/190 Test #117: pyMolAlign ............................. Passed 17.56 sec +181/190 Test #144: pySubstructLibrary ..................... Passed 11.56 sec +182/190 Test #151: pyGraphMolWrap ......................... Passed 16.08 sec +183/190 Test #114: pyDistGeomHelpers ...................... Passed 30.45 sec +184/190 Test #184: pythonTestDirML ........................ Passed 17.45 sec +185/190 Test #183: pythonTestDbCLI ........................ Passed 21.44 sec +186/190 Test #116: testO3AAlign ........................... Passed 41.25 sec +187/190 Test #5: testConcurrentQueue .................... Passed 50.09 sec +188/190 Test #27: graphmolTest1 .......................... Passed 59.06 sec +189/190 Test #113: testDistGeomHelpers .................... Passed 56.62 sec +190/190 Test #189: pythonTestDirChem ...................... Passed 113.57 sec + +100% tests passed, 0 tests failed out of 190 + +Total Test time (real) = 134.26 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=-j15 returned exit code 2 -make[1]: [debian/rules:126: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202009.4' fakeroot debian/rules binary dh binary --with python3 --buildsystem=cmake --parallel @@ -17599,7 +17388,7 @@ make[1]: Entering directory '/build/reproducible-path/rdkit-202009.4' dh_auto_install dh_auto_install: warning: Compatibility levels before 10 are deprecated (level 9 in use) - cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/reproducible-path/rdkit-202009.4/debian/tmp AM_UPDATE_INFO_DIR=no + cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/rdkit-202009.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202009.4 -B/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -17612,53 +17401,53 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/catch /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/INCHI-API /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/RingFamilies /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'External/catch/CMakeFiles/catch.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/RingFamilies /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202009.4/External/INCHI-API/python/noinchi.py /build/reproducible-path/rdkit-202009.4/rdkit/Chem/inchi.py make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'External/catch/CMakeFiles/catch.dir/build'. +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 0%] Built target ringdecomposerlib_support [ 0%] Built target coordgen_support [ 0%] Built target catch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend -[ 0%] Built target ringdecomposerlib_support make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDStreams /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 0%] Built target inchi_support make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build -[ 0%] Built target inchi_support +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build +make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDStreams/CMakeFiles/RDStreams.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -17676,15 +17465,15 @@ make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend -make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDBoost /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend +make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -17706,213 +17495,213 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 1%] Built target testConcurrentQueue make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDBoost/CMakeFiles/RDBoost.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 1%] Built target RDBoost -make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/testRDValue.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= -[ 2%] Built target testMatCalc +make[4]: Nothing to be done for 'Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/testDict.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/CMakeFiles/testMatrices.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/Query/CMakeFiles/testQuery.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build -[ 3%] Built target testRDValue -[ 3%] Built target testDict make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/Catalogs/CMakeFiles/Catalogs.dir/build'. +make[4]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 3%] Built target EigenSolvers make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 3%] Built target testMatrices -[ 3%] Built target testQuery -[ 4%] Built target SimDivPickers -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend -[ 4%] Built target Catalogs +make[4]: Nothing to be done for 'Code/Catalogs/CMakeFiles/Catalogs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 1%] Built target testConcurrentQueue make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= -make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build +make[4]: Nothing to be done for 'Code/Query/CMakeFiles/testQuery.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build'. +make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 4%] Built target rdBase +[ 1%] Built target RDBoost make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/DataStructs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build +make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 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Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend -make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend +make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build'. +make[4]: Nothing to be done for 'Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 6%] Built target testSimDivPickers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build +[ 6%] Built target rdBase make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build +make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testFPB.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testMultiFPB.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testMultiFPB.dir/build'. +make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testDataStructs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 6%] Built target testFPB make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 6%] Built target InfoTheory -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testDataStructs.dir/build'. +make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/RDGeometryLib.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 6%] Built target testSimDivPickers +[ 6%] Built target testFPB +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 6%] Built target testMultiFPB -[ 6%] Built target pickersTestsCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 6%] Built target InfoTheory +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 7%] Built target testDataStructs +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build +make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend +[ 7%] Built target pickersTestsCatch make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ML/Data /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= -[ 7%] Built target testDataStructs -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/RDGeometryLib.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 8%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend +[ 8%] Built target Clustering make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/Numerics/CMakeFiles/testConrec.dir/build'. +make[4]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build -[ 8%] Built target geometryTestsCatch make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/testGrid.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -17920,16 +17709,20 @@ make[4]: Nothing to be done for 'Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/Numerics/CMakeFiles/testConrec.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Geometry/CMakeFiles/testTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 9%] Built target testConrec -[ 9%] Built target Clustering -[ 9%] Built target testGrid -[ 9%] Built target Alignment +[ 8%] Built target rdMetricMatrixCalc +[ 8%] Built target geometryTestsCatch +[ 8%] Built target testGrid +[ 8%] Built target Alignment make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend +[ 9%] Built target testConrec make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend [ 9%] Built target ChemicalFeatures make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend @@ -17944,6 +17737,13 @@ make[4]: Nothing to be done for 'Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 10%] Built target rdGeometry +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 11%] Built target rdSimDivPickers +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -17952,112 +17752,94 @@ make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 10%] Built target testChemicalFeatures -[ 10%] Built target testAlignment make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build +[ 13%] Built target cDataStructs make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build'. +make[4]: Nothing to be done for 'Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build'. +make[4]: Nothing to be done for 'Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 10%] Built target rdMetricMatrixCalc make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 11%] Built target rdSimDivPickers -[ 13%] Built target cDataStructs -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/Data/CMakeFiles/cQuantize.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 13%] Built target cQuantize +[ 13%] Built target testAlignment +[ 13%] Built target testChemicalFeatures make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/GraphMol.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 13%] Built target cQuantize [ 13%] Built target rdInfoTheory [ 17%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend +[ 17%] Built target rdAlignment make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= -[ 17%] Built target rdAlignment -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build +make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -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-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 17%] Built target Trajectory -make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' @@ -18066,259 +17848,282 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 18%] Built target PartialCharges -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend -[ 18%] Built target MolInterchange -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build +[ 17%] Built target Trajectory +make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend +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-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build'. -make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 18%] Built target PartialCharges make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 18%] Built target MolInterchange +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend +make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend +[ 18%] Built target rdChemicalFeatures +[ 18%] Built target SubstructMatch +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 19%] Built target MolCatalog +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= +[ 19%] Built target Subgraphs make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend [ 20%] Built target rdqueries -[ 20%] Built target SubstructMatch -[ 20%] Built target Subgraphs -[ 20%] Built target rdChemicalFeatures -[ 20%] Built target SLNParse +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 20%] Built target SLNParse +[ 21%] Built target SmilesParse +make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 20%] Built target Optimizer -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend -[ 21%] Built target SmilesParse make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 24%] Built target CIPLabeler cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build +make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build -[ 21%] Built target rdtrajectory -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= +[ 24%] Built target Optimizer +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= -[ 24%] Built target CIPLabeler +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build'. +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 24%] Built target rdtrajectory +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= -[ 24%] Built target rdPartialCharges -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend -[ 24%] Built target rdMolInterchange -make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 25%] Built target testOptimizer make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 26%] Built target rdSLNParse -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend -[ 26%] Built target rdMolCatalog make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= -make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend +make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build +[ 24%] Built target MolTransforms +make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build +[ 24%] Built target rdPartialCharges +make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build +[ 24%] Built target rdMolInterchange +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build +[ 25%] Built target smiTest2 +[ 25%] Built target rdMolCatalog +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build'. +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build'. +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 26%] Built target graphmolcpTest -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/test-valgrind.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 26%] Built target graphmolqueryTest -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend -[ 26%] Built target graphmolIterTest -[ 26%] Built target graphmolMemTest1 +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 25%] Built target graphmolcpTest make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend +[ 25%] Built target graphmolqueryTest 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= -[ 26%] Built target test-valgrind +[ 25%] Built target graphmolMemTest1 +[ 25%] Built target graphmolIterTest make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= +make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend +[ 26%] Built target test-valgrind +[ 26%] Built target testSubgraphs2 make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend +make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend +[ 26%] Built target smaTest1 +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= [ 26%] Built target ChemTransforms -make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 27%] Built target smiTest2 -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 27%] Built target smaTest1 -make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend -[ 28%] Built target testSubgraphs2 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= +make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build +make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build +[ 26%] Built target testSubgraphs1 +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build +make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build +[ 27%] Built target FilterCatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 29%] Built target Fingerprints +make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= +make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/ForceField/CMakeFiles/ForceField.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 28%] Built target testSubgraphs1 -[ 31%] Built target ForceField make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend -make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 30%] Built target testOptimizer +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= -[ 32%] Built target FilterCatalog -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= +[ 30%] Built target testPartialCharges +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build @@ -18326,256 +18131,239 @@ make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build -[ 32%] Built target testPartialCharges -[ 32%] Built target rdCIPLabeler -[ 32%] Built target ReducedGraphs +[ 31%] Built target rdSLNParse +[ 31%] Built target ReducedGraphs +[ 31%] Built target MolChemicalFeatures +[ 31%] Built target testSLNParse +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend +[ 31%] Built target rdCIPLabeler +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend -[ 34%] Built target Fingerprints -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= -make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 34%] Built target MolChemicalFeatures -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend -[ 34%] Built target testSLNParse make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 35%] Built target FragCatalog -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 35%] Built target MolTransforms -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend -make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 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-f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build -[ 35%] Built target Abbreviations +[ 31%] Built target Abbreviations make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend +[ 32%] Built target FragCatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build'. +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build -[ 38%] Built target testCIPLabeler -[ 38%] Built target rdMHFPFingerprint -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build -[ 39%] Built target testReducedGraphs -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build +[ 32%] Built target rdMHFPFingerprint make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 40%] Built target rdfiltercatalog +make[4]: Nothing to be done for 'Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build -[ 41%] Built target rdFingerprintGenerator make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 42%] Built target rdMolChemicalFeatures -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build'. +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 43%] Built target SubstructLibrary -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend -[ 44%] Built target ForceFieldHelpers -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 -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +[ 33%] Built target rdfiltercatalog +[ 36%] Built target testCIPLabeler make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= -[ 45%] Built target rdAbbreviations -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build +make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 45%] Built target rdReducedGraphs -[ 47%] Built target rdchem +make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build +[ 37%] Built target rdFingerprintGenerator make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 47%] Built target rdForceFieldHelpers -[ 47%] Built target rdForceField make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build'. +make[4]: Nothing to be done for 'Code/ForceField/CMakeFiles/ForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/DistGeom/CMakeFiles/DistGeometry.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build -[ 47%] Built target rdSubstructLibrary -[ 48%] 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= +[ 38%] Built target testReducedGraphs +[ 39%] Built target rdAbbreviations +make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build +[ 40%] Built target rdMolChemicalFeatures +[ 43%] Built target ForceField +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +[ 44%] Built target SubstructLibrary +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/DistGeom/CMakeFiles/testDistGeom.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 48%] Built target MolAlign +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build +[ 44%] Built target MolAlign +[ 44%] Built target ShapeHelpers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 44%] Built target rdReducedGraphs +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +[ 46%] Built target rdchem make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend -[ 48%] Built target ShapeHelpers make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend -[ 49%] Built target testDistGeom make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 47%] Built target rdMolTransforms +[ 47%] Built target rdSubstructLibrary +[ 48%] Built target ForceFieldHelpers +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 -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 49%] Built target DistGeomHelpers -[ 50%] Built target rdMolTransforms +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build -[ 51%] Built target DistGeom make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 51%] Built target rdShapeHelpers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build'. +make[4]: Nothing to be done for 'Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/DistGeom/CMakeFiles/DistGeometry.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 48%] Built target rdShapeHelpers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build +[ 48%] Built target rdForceField +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 48%] Built target rdForceFieldHelpers +[ 49%] 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 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/build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= +[ 49%] Built target Depictor make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 51%] Built target O3AAlign -[ 51%] Built target Depictor +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd 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+make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 50%] Built target testDistGeom +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 50%] Built target DistGeomHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -18584,6 +18372,7 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 51%] Built target DistGeom [ 52%] Built target rdDepictor [ 55%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend @@ -18591,64 +18380,69 @@ make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake --color= -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -18656,10 +18450,10 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build'. @@ -18667,202 +18461,214 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/hanoiTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 55%] Built target chiralityTestsCatch -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend -[ 55%] Built target graphmolSGroupCatch -[ 56%] Built target resMolSupplierTest -[ 56%] Built target hanoiTest -make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend -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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= -[ 56%] Built target graphmoltestChirality -make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend +make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/molBundleTest.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/testSGroup.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 55%] Built target graphmolSGroupCatch make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build'. -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 55%] Built target chiralityTestsCatch +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-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= +[ 56%] Built target resMolSupplierTest +[ 56%] Built target hanoiTest +[ 57%] Built target molBundleTest +[ 57%] Built target graphmoltestChirality +[ 57%] Built target testSGroup +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 56%] Built target testSGroup +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= +[ 58%] Built target graphmolAdjustQueryCatch +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend -[ 57%] Built target graphmolAdjustQueryCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend -[ 58%] Built target graphmolTestsCatch -[ 59%] Built target graphmolMolOpsTest make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= +[ 59%] Built target graphmolTestsCatch [ 59%] Built target graphmolTest1 -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend -[ 60%] Built target graphmoltestPickler +[ 60%] Built target graphmolMolOpsTest [ 60%] Built target graphmoltestPicklerGlobalSetting +[ 61%] Built target graphmoltestPickler +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend -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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= +make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= +make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build +make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build -make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build 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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/CMakeFiles/molBundleTest.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 61%] Built target smiTest1 +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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 60%] Built target smiTest1 -make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend -[ 61%] Built target cxsmilesTest -[ 62%] Built target molBundleTest -make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= +[ 62%] Built target cxsmilesTest +make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 62%] Built target smiTestCatch -make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend -[ 62%] Built target testDepictor -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 63%] Built target testSequence -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-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend +make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= -[ 64%] Built target testExtendedStereoParsing +[ 64%] Built target testMolWriter +[ 65%] Built target testExtendedStereoParsing +[ 65%] Built target testTplParser +make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend +make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= -[ 65%] Built target testMolWriter -make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 65%] Built target testDepictor +make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 65%] Built target testMol2ToMol make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= +make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= -[ 65%] Built target testMolSupplier -make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend -[ 66%] Built target fileParsersTest1 -make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= +[ 65%] Built target smiTestCatch +[ 65%] Built target testMolSupplier +make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 66%] Built target testMultithreadedMolSupplier -[ 67%] Built target testGeneralFileReader -make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend -make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend +[ 66%] Built target fileParsersTest1 +make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= +[ 67%] Built target testGeneralFileReader +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= +[ 67%] Built target testMultithreadedMolSupplier +make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build +make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -18870,25 +18676,17 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build'. +make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build -[ 67%] Built target testTplParser -make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend -[ 67%] Built target testMol2ToMol -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= +make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -18896,203 +18694,194 @@ make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 67%] Built target substructTestCatch -make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= -[ 68%] Built target testPropertyLists make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend +[ 68%] Built target testPropertyLists +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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= [ 68%] Built target testChemTransforms -[ 68%] Built target fileParsersCatchTest -make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend -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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend [ 68%] Built target chemTransformsTestCatch -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= +[ 68%] Built target fileParsersCatchTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= -[ 68%] Built target testSubstructMatch +make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build -[ 68%] Built target filterCatalogTest +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= +[ 68%] Built target testSubstructMatch make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build +[ 68%] Built target testMHFPFingerprint +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/testCoordGen.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 68%] Built target testCoordGen -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-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= -[ 68%] Built target testFragCatalog +[ 68%] Built target filterCatalogTest make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend +[ 68%] Built target testCoordGen +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= -[ 68%] Built target rdfragcatalog -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 69%] Built target testUFFForceField +[ 69%] Built target testFingerprintGenerators 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build +[ 69%] Built target testFragCatalog +make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend +[ 70%] Built target testUFFForceField +make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend +[ 70%] Built target rdfragcatalog +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= -[ 69%] Built target testMMFFForceField -make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= +[ 70%] Built target fpTestCatch +[ 70%] Built target testMMFFForceField +make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 69%] Built target testMHFPFingerprint -make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend +make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Built target testFingerprintGenerators -make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build'. +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build +make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= -[ 70%] Built target fpTestCatch -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= -[ 70%] Built target testFingerprints -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build'. +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build +[ 70%] Built target testFingerprints make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build +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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 70%] Built target testMMFFForceFieldHelpersMultiThread -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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= -[ 71%] Built target testMMFFForceFieldHelpers -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend -[ 71%] Built target testUFFForceFieldHelpers -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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build +make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build -[ 71%] Built target testFeatures -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 70%] Built target testMMFFForceFieldHelpersMultiThread +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build -[ 71%] Built target testDistGeomHelpers -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend +[ 70%] Built target testUFFForceFieldHelpers +make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend +[ 71%] Built target testMMFFForceFieldHelpers make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build +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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 72%] Built target testMolCatalog +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 72%] Built target MMPA +[ 71%] Built target testFeatures +[ 71%] Built target testDistGeomHelpers +[ 71%] Built target MMPA make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend 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-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build +[ 72%] Built target trajectoryTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 73%] Built target trajectoryTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 73%] Built target testMolCatalog +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build +[ 73%] Built target substructLibraryTest [ 74%] Built target FMCS make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend @@ -19106,88 +18895,86 @@ cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 74%] Built target testAbbreviations -[ 75%] Built target molInterchangeTest1 -[ 75%] Built target substructLibraryTest +make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build +[ 75%] Built target molInterchangeTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' 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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 77%] Built target rdmolfiles make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 77%] Built target rdDistGeom +[ 75%] Built target testAbbreviations +[ 75%] Built target rdDistGeom make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 77%] Built target testMMPA -[ 78%] Built target rdMMPA -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 76%] Built target rdMMPA +[ 76%] Built target testMMPA make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 78%] Built target rdFMCS -[ 78%] Built target FMCStest -[ 78%] Built target testFMCS +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 76%] Built target rdFMCS make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 76%] Built target FMCStest +[ 76%] Built target testFMCS +[ 78%] Built target rdmolfiles +[ 79%] Built target RGroupDecomposition make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 79%] Built target RGroupDecomposition -[ 81%] Built target Descriptors -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend -[ 81%] Built target testMolTransforms -make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= -[ 81%] Built target testCrystalForceField -[ 81%] Built target testShapeHelpers +[ 81%] Built target Descriptors make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend +[ 81%] Built target testMolTransforms make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend @@ -19198,73 +18985,83 @@ make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend -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-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= +[ 81%] Built target testCrystalForceField make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= +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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake --color= +[ 81%] Built target testShapeHelpers make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +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-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make 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directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build'. @@ -19272,77 +19069,69 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 81%] Built target testMORSE [ 81%] Built target testRGroupDecomp -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend +make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build +[ 81%] Built target testMORSE make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/depend -[ 82%] Built target testAUTOCORR2D make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend -[ 82%] Built target testAUTOCORR3D -[ 82%] Built target testGETAWAY -[ 82%] Built target testATF +[ 81%] Built target testGETAWAY +[ 81%] Built target testPBF +[ 82%] Built target testAUTOCORR2D make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend -[ 82%] Built target testEEM make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend +[ 82%] Built target testAUTOCORR3D make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend -[ 82%] Built target testPBF make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend +[ 82%] Built target testEEM +[ 82%] Built target testATF +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build -[ 83%] Built target testBCUT +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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= -[ 83%] Built target testRDFcustom -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 82%] Built target testRDFcustom +[ 82%] Built target testRDF +[ 83%] Built target testBCUT [ 83%] Built target test3D -[ 83%] Built target testCoulombMat make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 83%] Built target testCoulombMat [ 83%] Built target testDescriptors make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 83%] Built target testRDF make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -19351,12 +19140,19 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' [ 83%] Built target testWHIM [ 86%] Built target ChemReactions make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +[ 87%] Built target MolHash make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend @@ -19365,136 +19161,141 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= +[ 87%] Built target rdRGroupDecomposition make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= -[ 87%] Built target MolHash +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend +[ 87%] Built target rdMolDescriptors make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 87%] Built target rdRGroupDecomposition -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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build'. +make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= -[ 87%] Built target rdMolDescriptors +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 87%] Built target rdMolAlign +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 87%] Built target molHashCatchTest +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build -[ 88%] Built target Deprotect -make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend -make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend -[ 88%] Built target molHashCatchTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --color= +[ 87%] Built target rdMolHash make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 88%] Built target Deprotect +make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend +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-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake --color= [ 88%] Built target MolEnumerator -[ 88%] Built target testReactionFingerprints make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend -[ 88%] Built target rxnTestCatch make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 88%] Built target testReactionFingerprints +[ 88%] Built target rxnTestCatch make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= -[ 88%] Built target rdMolHash [ 88%] Built target testReaction -[ 88%] Built target rdMolAlign -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= [ 88%] Built target testEnumeration -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build +[ 89%] Built target rdChemReactions make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build -[ 89%] Built target rdChemReactions make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build +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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 89%] Built target deprotectTest +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 89%] Built target testMolAlign +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 89%] Built target testO3AAlign [ 92%] Built target MolStandardize +[ 92%] Built target deprotectTest +[ 92%] Built target rdDeprotect make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend @@ -19503,77 +19304,76 @@ make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend 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-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend -[ 92%] Built target rdMolEnumerator -[ 92%] Built target rdDeprotect make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend 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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= +[ 92%] Built target rdMolEnumerator make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= [ 92%] Built target testMolEnumerator -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build +[ 94%] Built target MolDraw2D make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build'. +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build -make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build -[ 92%] Built target testO3AAlign -[ 92%] Built target testMolAlign -[ 92%] Built target molValidateTest -[ 93%] Built target molStandardizeTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build'. @@ -19587,110 +19387,99 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 94%] Built target molValidateTest make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 95%] Built target MolDraw2D -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend -[ 95%] Built target molTautomerTest -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend -[ 95%] Built target TautomerQuery -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend -make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend -[ 95%] Built target molNormalizeTest -[ 95%] Built target molFragmentTest -[ 95%] Built target molChargeTest -[ 95%] Built target molStandardizeSmallTest -[ 95%] Built target molStandardizeCatchTest -[ 96%] Built target rdMolStandardize -[ 97%] Built target ScaffoldNetwork +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +[ 94%] Built target molTautomerTest +[ 94%] Built target molChargeTest +[ 94%] Built target molNormalizeTest +[ 94%] Built target molStandardizeSmallTest +[ 94%] Built target molFragmentTest +[ 95%] Built target ScaffoldNetwork +[ 96%] Built target molStandardizeTest 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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend +[ 96%] Built target TautomerQuery +[ 96%] Built target molStandardizeCatchTest +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend +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-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202009.4 /build/reproducible-path/rdkit-202009.4/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build +[ 97%] Built target rdMolStandardize make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +[ 97%] Built target moldraw2DRxnTest1 +[ 97%] Built target moldraw2DTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-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-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build'. +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 97%] Built target rdTautomerQuery -[ 97%] Built target rdScaffoldNetwork make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build'. +make[4]: Nothing to be done for 'Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 97%] Built target testScaffoldNetwork -[ 97%] Built target moldraw2DRxnTest1 -make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 98%] Built target tautomerQueryTestCatch -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build -[ 98%] Built target moldraw2DTestCatch -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' -[ 99%] Built target rdMolDraw2D +[ 97%] Built target rdScaffoldNetwork make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' +[ 97%] Built target rdTautomerQuery +[ 97%] Built target testScaffoldNetwork +[ 98%] Built target tautomerQueryTestCatch +[ 99%] Built target rdMolDraw2D [ 99%] Built target rdmolops [100%] Built target moldraw2DTest1 make[3]: Leaving directory '/build/reproducible-path/rdkit-202009.4/obj-x86_64-linux-gnu' @@ -22255,27 +22044,27 @@ dh_installdeb -O--buildsystem=cmake -O--parallel dh_installdeb: warning: Compatibility levels before 10 are deprecated (level 9 in use) dh_gencontrol -O--buildsystem=cmake -O--parallel -dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package rdkit-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: package postgresql-13-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package postgresql-13-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package postgresql-13-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake -O--parallel dh_builddeb -O--buildsystem=cmake -O--parallel dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202009.4-1_amd64.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202009.4-1_amd64.deb'. +dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202009.4-1_all.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202009.4-1_all.deb'. -dpkg-deb: building package 'postgresql-13-rdkit' in '../postgresql-13-rdkit_202009.4-1_amd64.deb'. +dpkg-deb: building package 'librdkit1' in '../librdkit1_202009.4-1_amd64.deb'. dpkg-deb: building package 'librdkit1-dbgsym' in '../librdkit1-dbgsym_202009.4-1_amd64.deb'. -dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202009.4-1_all.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202009.4-1_amd64.deb'. +dpkg-deb: building package 'postgresql-13-rdkit' in '../postgresql-13-rdkit_202009.4-1_amd64.deb'. dpkg-deb: building package 'postgresql-13-rdkit-dbgsym' in '../postgresql-13-rdkit-dbgsym_202009.4-1_amd64.deb'. -dpkg-deb: building package 'librdkit1' in '../librdkit1_202009.4-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rdkit_202009.4-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -22283,12 +22072,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/514051/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/514051/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/844879 and its subdirectories -I: Current time: Sat Jan 6 08:17:30 -12 2024 -I: pbuilder-time-stamp: 1704572250 +I: removing directory /srv/workspace/pbuilder/514051 and its subdirectories +I: Current time: Sat Feb 8 17:04:06 +14 2025 +I: pbuilder-time-stamp: 1738983846