Tue Dec 17 20:39:19 UTC 2024 I: starting to build rdkit/unstable/amd64 on jenkins on '2024-12-17 20:39' Tue Dec 17 20:39:19 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_9/25943/console.log Tue Dec 17 20:39:19 UTC 2024 I: Downloading source for unstable/rdkit=202409.2-2 --2024-12-17 20:39:19-- http://deb.debian.org/debian/pool/main/r/rdkit/rdkit_202409.2-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3000 (2.9K) [text/prs.lines.tag] Saving to: ‘rdkit_202409.2-2.dsc’ 0K .. 100% 8.14M=0s 2024-12-17 20:39:19 (8.14 MB/s) - ‘rdkit_202409.2-2.dsc’ saved [3000/3000] Tue Dec 17 20:39:19 UTC 2024 I: rdkit_202409.2-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: rdkit Binary: python3-rdkit, rdkit-doc, rdkit-data, librdkit1t64, librdkit-dev, postgresql-17-rdkit Architecture: any all Version: 202409.2-2 Maintainer: Debichem Team Uploaders: Michael Banck , Andrius Merkys Homepage: http://www.rdkit.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/rdkit Vcs-Git: https://salsa.debian.org/debichem-team/rdkit.git Testsuite: autopkgtest Testsuite-Triggers: dpkg-dev, make Build-Depends: bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-numpy-dev, libboost-program-options-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo2-dev, libcoordgen-dev, libeigen3-dev, libfreetype-dev, libinchi-dev (>= 1.07.1+dfsg-2), libmaeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-myst-parser, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-pytest, python3-recommonmark, python3-sphinx, python3-sqlalchemy, rapidjson-dev, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended Package-List: librdkit-dev deb libdevel optional arch=any librdkit1t64 deb libs optional arch=any postgresql-17-rdkit deb database optional arch=any python3-rdkit deb python optional arch=any rdkit-data deb science optional arch=all rdkit-doc deb doc optional arch=all Checksums-Sha1: 7071422f42cc0c9d12e11d4e45bce49d60b68b7b 62272108 rdkit_202409.2.orig.tar.xz 71e8c8b661936293d012d907de6dafbf2d01b334 39312 rdkit_202409.2-2.debian.tar.xz Checksums-Sha256: 108bb2e5dfedf971a3147a9cfe430e0edf0a686d7825e3c680dc9fe42855924a 62272108 rdkit_202409.2.orig.tar.xz 061fb4bd4ed164b8b007335ef13068d56ebdf757cdd59b4f41e7e1726e150bf8 39312 rdkit_202409.2-2.debian.tar.xz Files: edb6d2cee84cb285a8a6388c36fc3411 62272108 rdkit_202409.2.orig.tar.xz 5c40a5c042fb53196ac92facfb259ab5 39312 rdkit_202409.2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEnKh3dJ+rLk+paGLs3GhqJ7Q0gbAFAmdHbtEACgkQ3GhqJ7Q0 gbCFyw/+ObwozPD6Bv/D7FkESB89fow4lJeonmLFg80d4OV3NIInKcM5pl1+vC0K +zfz5a5SqPe2eYXAjzzQ0dm5jL4v+0n0ngeSb8Zut62LUPu+Wm6Y+eQAJspxGJdR rwM+ruzIj4A8fN3SVD/Cqr+Lg2t1dMWQnkTIWdIUIbyno2qTE74yRwVM041HFLqA 0yDe5wnM4Gu09EhLiFVAG75SLH8wi89bZ/fZDrCWnjMzeR+0YnFkgpjeE8O6PSoU UGlNXZSVM3aQovW5OPcG0QCzvjsQTgPSjVgeNPQUus31Jv94eW0pmCo7YqDjOTuI 7w8GTBBXg9FzlH873VFTRRH+GOi6UIkHPSyZOmcI/n6JtGsYw1x3THa0SBQKJqYE 4u6lOrAOMkgauu4GKCmjkXEOtIVPQu6ppVtyay/fFhyzQLv+Xcz2AyVTij9THiED x6LJIFhtEUbSSaHAuwiISDKypaIimqPDLZJvVvKF+sdc9y3zbJOfW2tL8yF6Q/5x YIS5y2X7ReEQrb1Jxze/SOFxvxdE19H6mw453A2OJWp3txGkgQXI0tdqywT5zQfv e2GoopT/KqOCxkKguXy05g2wsTgDl3WoIKqxlGTExZRbdKQig7jhIgpRFtsroug/ LENZBNk2a64WEptaDYBPFNje5x378/KJ8F0agGhIUFGhcHRJgZg= =ghIi -----END PGP SIGNATURE----- Tue Dec 17 20:39:19 UTC 2024 I: Checking whether the package is not for us Tue Dec 17 20:39:19 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Tue Dec 17 20:39:19 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Tue Dec 17 21:19:44 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 17 08:39:23 -12 2024 I: pbuilder-time-stamp: 1734467963 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [rdkit_202409.2-2.dsc] I: copying [./rdkit_202409.2.orig.tar.xz] I: copying [./rdkit_202409.2-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 27 19:11:13 2024 gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rdkit_202409.2-2.dsc: no acceptable signature found dpkg-source: info: extracting rdkit in rdkit-202409.2 dpkg-source: info: unpacking rdkit_202409.2.orig.tar.xz dpkg-source: info: unpacking rdkit_202409.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying NoDownloads.patch dpkg-source: info: applying postgres_Makefile_fixes.patch dpkg-source: info: applying sphinx_imgconverter.patch dpkg-source: info: applying postgres_alternative_test_outputs.patch dpkg-source: info: applying sphinx_compile_fixes.patch dpkg-source: info: applying extra_float_digits dpkg-source: info: applying postgres_cmakelists_fixes.patch dpkg-source: info: applying disable_pgsql_test.patch dpkg-source: info: applying fix_inchi_linking.patch dpkg-source: info: applying disable_inchi_test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3972870/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='a35516a897534845bccdbd33d9b729ca' 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='3972870' PS1='# ' PS2='> ' 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.wWec19YJ/pbuilderrc_2WxU --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wWec19YJ/b1 --logfile b1/build.log rdkit_202409.2-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3972870/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-numpy-dev, libboost-program-options-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo2-dev, libcoordgen-dev, libeigen3-dev, libfreetype-dev, libinchi-dev (>= 1.07.1+dfsg-2), libmaeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-myst-parser, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-pytest, python3-recommonmark, python3-sphinx, python3-sqlalchemy, rapidjson-dev, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on catch2; however: Package catch2 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on latexmk; however: Package latexmk is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-numpy-dev; however: Package libboost-numpy-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-python-dev; however: Package libboost-python-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libcairo2-dev; however: Package libcairo2-dev is not installed. pbuilder-satisfydepends-dummy depends on libcoordgen-dev; however: Package libcoordgen-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libfreetype-dev; however: Package libfreetype-dev is not installed. pbuilder-satisfydepends-dummy depends on libinchi-dev (>= 1.07.1+dfsg-2); however: Package libinchi-dev is not installed. pbuilder-satisfydepends-dummy depends on libmaeparser-dev; however: Package libmaeparser-dev is not installed. pbuilder-satisfydepends-dummy depends on librsvg2-bin; however: Package librsvg2-bin is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on postgresql-server-dev-all; however: Package postgresql-server-dev-all is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-myst-parser; however: Package python3-myst-parser is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pil | python3-imaging; however: Package python3-pil is not installed. Package python3-imaging is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-recommonmark; however: Package python3-recommonmark is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sqlalchemy; however: Package python3-sqlalchemy is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bison{a} bsdextrautils{a} ca-certificates{a} catch2{a} clang-19{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} girepository-tools{a} groff-base{a} hicolor-icon-theme{a} icu-devtools{a} imagemagick{a} imagemagick-7-common{a} imagemagick-7.q16{a} intltool-debian{a} latexmk{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libblkid-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcatch2-dev{a} libclang-common-19-dev{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcoordgen-dev{a} libcoordgen3{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontbox-java{a} libfontconfig-dev{a} libfontconfig1{a} libfontenc1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgc1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libgio-2.0-dev{a} libgio-2.0-dev-bin{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice-dev{a} libice6{a} libicu-dev{a} libicu72{a} libimagequant0{a} libinchi-dev{a} libinchi1.07{a} libio-pty-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm19{a} liblqr-1-0{a} libltdl7{a} liblua5.4-0{a} liblzo2-2{a} libmaeparser-dev{a} libmaeparser1{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-7.q16-10{a} libmagickwand-7.q16-10{a} libmount-dev{a} libmpfi0{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnsl2{a} libnuma1{a} libobjc-14-dev{a} libobjc4{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpdfbox-java{a} libpfm4{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpotrace0{a} libpq-dev{a} libpq5{a} libproc2-0{a} libpsl5t64{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libraqm0{a} libraw23t64{a} libreadline8t64{a} librhash1{a} librsvg2-2{a} librsvg2-bin{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsm-dev{a} libsm6{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libsynctex2{a} libsysprof-capture-4-dev{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxi6{a} libxml2{a} libxml2-dev{a} libxmu6{a} libxpm4{a} libxrender-dev{a} libxrender1{a} libxt6t64{a} libyaml-0-2{a} libz3-4{a} libz3-dev{a} libzzip-0-13t64{a} llvm-19{a} llvm-19-dev{a} llvm-19-linker-tools{a} llvm-19-runtime{a} llvm-19-tools{a} m4{a} man-db{a} media-types{a} native-architecture{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} postgresql-client-17{a} postgresql-client-common{a} postgresql-common{a} postgresql-server-dev-17{a} postgresql-server-dev-all{a} preview-latex-style{a} procps{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-commonmark{a} python3-dateutil{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-greenlet{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markdown-it{a} python3-markupsafe{a} python3-mdit-py-plugins{a} python3-mdurl{a} python3-minimal{a} python3-more-itertools{a} python3-myst-parser{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pygments{a} python3-pytest{a} python3-recommonmark{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sqlalchemy{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sphinx-common{a} ssl-cert{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: apvlv atril binfmt-support bzip2-doc curl default-jre dvisvgm e2fsprogs evince fonts-texgyre fonts-texgyre-math fonts-urw-base35 ghostscript gv javascript-common krb5-locales libarchive-cpio-perl libclang-rt-19-dev libfile-mimeinfo-perl libfl-dev libgdk-pixbuf2.0-bin libgpm2 libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libldap-common libltdl-dev libmagickcore-7.q16-10-extra libmail-sendmail-perl libnet-dbus-perl libpng-tools librsvg2-common libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern logrotate lynx mupdf netpbm okular psmisc publicsuffix python3-bottleneck python3-bs4 python3-html5lib python3-lxml python3-matplotlib python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-scipy python3-sqlalchemy-ext python3-tables qpdfview qpdfview-ps-plugin ruby systemd texlive-plain-generic tipa tk viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 369 newly installed, 0 to remove and 0 not upgraded. Need to get 418 MB of archives. After unpacking 2160 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b3 [423 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.19.3-1 [11.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [15.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.3-1 [489 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 liblqr-1-0 amd64 0.4.2-2.1+b2 [29.5 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-8 [393 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libraw23t64 amd64 0.21.3-1+b1 [390 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 imagemagick-7-common all 8:7.1.1.39+dfsg1-3 [66.9 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libmagickcore-7.q16-10 amd64 8:7.1.1.39+dfsg1-3 [1845 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libmagickwand-7.q16-10 amd64 8:7.1.1.39+dfsg1-3 [338 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 postgresql-client-common all 267 [36.5 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 ssl-cert all 1.1.3 [16.8 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0045 [45.2 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 postgresql-common all 267 [170 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.8-3 [2162 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-4 [256 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.8-3 [677 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-3 [200 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-3 [723 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libcatch2-dev amd64 3.7.1-0.4 [613 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 catch2 all 3.7.1-0.4 [5052 B] Get: 93 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.5-1 [26.0 MB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.5-1 [13.2 MB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libgc1 amd64 1:8.2.8-1 [247 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libobjc4 amd64 14.2.0-11 [42.8 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libobjc-14-dev amd64 14.2.0-11 [170 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libclang-common-19-dev amd64 1:19.1.5-1 [739 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 llvm-19-linker-tools amd64 1:19.1.5-1 [1260 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.5-1 [7615 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 clang-19 amd64 1:19.1.5-1 [116 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.2-1 [2267 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.2-1 [11.9 MB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.21 [88.9 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 124 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-3 [1600 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.21 [919 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 136 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241217 [113 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.9.8+ds-2+b3 [5011 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 native-architecture all 0.2.3 [2108 B] Get: 149 http://deb.debian.org/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.82.4-1 [139 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 girepository-tools amd64 2.82.4-1 [145 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5+b1 [210 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 imagemagick-7.q16 amd64 8:7.1.1.39+dfsg1-3 [726 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 imagemagick amd64 8:7.1.1.39+dfsg1-3 [20.0 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.18 [32.5 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 158 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [157 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [49.1 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.7 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [114 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [8492 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20241115-1 [22.7 MB] Get: 185 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 latexmk all 1:4.85-1 [501 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 188 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.2-12 [47.3 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libblkid-dev amd64 2.40.2-12 [204 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4 [234 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4 [235 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4 [240 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-4 [245 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-4 [230 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4 [333 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4 [373 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-4 [239 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 201 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-4 [330 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5+b1 [10.4 MB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-4 [346 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4 [261 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 206 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83.0 amd64 1.83.0-4 [320 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libboost-numpy1.83.0 amd64 1.83.0-4 [242 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libboost-numpy1.83-dev amd64 1.83.0-4 [246 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B] Get: 210 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4 [347 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4 [375 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 213 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.8-3 [2154 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.8-3 [5134 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.7-1 [9976 B] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.8-3 [505 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-2 [30.3 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.7-1 [26.1 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-4 [328 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 225 http://deb.debian.org/debian unstable/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get: 226 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-4 [230 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-4 [231 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 229 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-4 [269 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-4 [276 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 232 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libcairo-script-interpreter2 amd64 1.18.2-2 [58.8 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.44-3 [366 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-1.1+b1 [414 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.7-1 [370 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.44-5 [260 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.44-5 [248 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.44-5 [60.4 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.44-5 [790 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.7-3+b1 [160 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libmount-dev amd64 2.40.2-12 [29.1 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libsysprof-capture-4-dev amd64 47.2-1 [47.7 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev amd64 2.82.4-1 [1678 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libglib2.0-data all 2.82.4-1 [1276 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libglib2.0-bin amd64 2.82.4-1 [127 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev-bin amd64 2.82.4-1 [163 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.82.4-1 [52.0 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev amd64 2.82.4-1 [52.7 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libpixman-1-dev amd64 0.44.0-3 [11.4 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 263 http://deb.debian.org/debian unstable/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libxcb-render0-dev amd64 1.17.0-2+b1 [118 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0-dev amd64 1.17.0-2+b1 [108 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b2 [104 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b3 [35.9 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libcairo2-dev amd64 1.18.2-2 [43.0 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libcoordgen3 amd64 3.0.2-1+b2 [225 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libcoordgen-dev amd64 3.0.2-1+b2 [46.9 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-11 [836 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libinchi1.07 amd64 1.07.1+dfsg-6 [557 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libinchi-dev amd64 1.07.1+dfsg-6 [19.5 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.7-1+b1 [147 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libmaeparser1 amd64 1.3.1-1+b2 [94.0 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libmaeparser-dev amd64 1.3.1-1+b2 [13.7 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git83-g91970fe-1 [368 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 libpq5 amd64 17.2-1 [223 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 libpq-dev amd64 17.2-1 [147 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 librsvg2-2 amd64 2.59.2+dfsg-1 [1854 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 librsvg2-bin amd64 2.59.2+dfsg-1 [2015 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 libz3-dev amd64 4.13.3-1 [107 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 llvm-19-runtime amd64 1:19.1.5-1 [550 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 llvm-19 amd64 1:19.1.5-1 [16.4 MB] Get: 317 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 llvm-19-tools amd64 1:19.1.5-1 [510 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 llvm-19-dev amd64 1:19.1.5-1 [43.2 MB] Get: 321 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get: 323 http://deb.debian.org/debian unstable/main amd64 postgresql-client-17 amd64 17.2-1 [2010 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 postgresql-server-dev-17 amd64 17.2-1 [1316 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 postgresql-server-dev-all amd64 267 [20.8 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.16.0-1 [114 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 331 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 python3-commonmark all 0.9.1-7 [45.4 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 python3-greenlet amd64 3.1.0-1+b1 [179 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 341 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 342 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1.1 [120 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get: 345 http://deb.debian.org/debian unstable/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 python3-mdit-py-plugins all 0.4.2-1 [32.4 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-2 [616 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.2.3-4 [112 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-2 [468 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 python3-myst-parser all 4.0.0-1 [78.7 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.2-1 [31.0 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5+b1 [7307 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 python3-sqlalchemy all 2.0.32+ds1-1 [1196 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 tex-gyre all 20180621-6 [6209 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2024.20241115-1 [4991 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 369 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] Fetched 418 MB in 6s (74.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../00-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../01-flex_2.6.4-8.2+b3_amd64.deb ... Unpacking flex (2.6.4-8.2+b3) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../02-libfftw3-double3_3.3.10-2+b1_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.10-2+b1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../03-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../04-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../05-libpng16-16t64_1.6.44-3_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. 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Selecting previously unselected package libde265-0:amd64. Preparing to unpack .../14-libde265-0_1.0.15-1+b2_amd64.deb ... Unpacking libde265-0:amd64 (1.0.15-1+b2) ... Selecting previously unselected package libheif-plugin-libde265:amd64. Preparing to unpack .../15-libheif-plugin-libde265_1.19.3-1_amd64.deb ... Unpacking libheif-plugin-libde265:amd64 (1.19.3-1) ... Selecting previously unselected package libheif1:amd64. Preparing to unpack .../16-libheif1_1.19.3-1_amd64.deb ... Unpacking libheif1:amd64 (1.19.3-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../17-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../18-libjpeg62-turbo_1%3a2.1.5-3+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../19-liblcms2-2_2.16-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../20-libglib2.0-0t64_2.82.4-1_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.4-1) ... Selecting previously unselected package liblqr-1-0:amd64. Preparing to unpack .../21-liblqr-1-0_0.4.2-2.1+b2_amd64.deb ... Unpacking liblqr-1-0:amd64 (0.4.2-2.1+b2) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../22-libltdl7_2.4.7-8_amd64.deb ... Unpacking libltdl7:amd64 (2.4.7-8) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../23-libopenjp2-7_2.5.0-2+b4_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.0-2+b4) ... Selecting previously unselected package libraw23t64:amd64. Preparing to unpack .../24-libraw23t64_0.21.3-1+b1_amd64.deb ... Unpacking libraw23t64:amd64 (0.21.3-1+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../25-libdeflate0_1.22-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.22-1) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../26-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../27-libwebp7_1.4.0-0.1+b1_amd64.deb ... Unpacking libwebp7:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../28-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../29-libwebpdemux2_1.4.0-0.1+b1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../30-libwebpmux3_1.4.0-0.1+b1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../31-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../32-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../33-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../34-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../35-libx11-6_2%3a1.8.10-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../36-libxext6_2%3a1.3.4-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b2) ... Selecting previously unselected package libicu72:amd64. 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Preparing to unpack .../42-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../43-libio-pty-perl_1%3a1.20-1+b2_amd64.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../44-libipc-run-perl_20231003.0-2_all.deb ... Unpacking libipc-run-perl (20231003.0-2) ... Selecting previously unselected package netbase. Preparing to unpack .../45-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package postgresql-client-common. Preparing to unpack .../46-postgresql-client-common_267_all.deb ... Unpacking postgresql-client-common (267) ... Selecting previously unselected package openssl. Preparing to unpack .../47-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ssl-cert. Preparing to unpack .../48-ssl-cert_1.1.3_all.deb ... Unpacking ssl-cert (1.1.3) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../49-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../50-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../51-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package ucf. Preparing to unpack .../52-ucf_3.0045_all.deb ... Moving old data out of the way Unpacking ucf (3.0045) ... Selecting previously unselected package postgresql-common. Preparing to unpack .../53-postgresql-common_267_all.deb ... Adding 'diversion of /usr/bin/pg_config to /usr/bin/pg_config.libpq-dev by postgresql-common' Unpacking postgresql-common (267) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../54-libpython3.12-minimal_3.12.8-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-3) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../55-python3.12-minimal_3.12.8-3_amd64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:amd64 (3.12.8-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (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 ... 22253 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package tzdata. Preparing to unpack .../02-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../03-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../04-libcom-err2_1.47.2~rc1-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../07-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../08-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../14-libpython3.12-stdlib_3.12.8-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-3) ... Selecting previously unselected package python3.12. 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Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libffi-dev:amd64 (3.4.6-1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libpcre2-16-0:amd64 (10.44-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up rapidjson-dev (1.1.0+dfsg2-7.3) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libmaeparser1:amd64 (1.3.1-1+b2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Dec 17 20:44:08 UTC 2024. Universal Time is now: Tue Dec 17 20:44:08 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4) ... Setting up libsysprof-capture-4-dev:amd64 (47.2-1) ... Setting up libboost-serialization1.83.0:amd64 (1.83.0-4) ... Setting up xtrans-dev (1.4.0-1) ... Setting up libboost-numpy1.83.0 (1.83.0-4) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libpcre2-32-0:amd64 (10.44-5) ... Setting up libglib2.0-0t64:amd64 (2.82.4-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libglib2.0-data (2.82.4-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libpfm4:amd64 (4.13.0+git83-g91970fe-1) ... Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Setting up libsqlite3-dev:amd64 (3.46.1-1) ... Setting up libboost-program-options-dev:amd64 (1.83.0.2+b2) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libboost-chrono1.83.0t64:amd64 (1.83.0-4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libteckit0:amd64 (2.5.12+ds1-1+b1) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up uuid-dev:amd64 (2.40.2-12) ... Setting up libapache-pom-java (33-2) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-5) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:amd64 (3.3.2-2) ... Setting up libpng16-16t64:amd64 (1.6.44-3) ... Setting up autopoint (0.22.5-3) ... Setting up libboost-numpy1.83-dev (1.83.0-4) ... Setting up libmpfi0:amd64 (1.5.4+ds-4) ... Setting up icu-devtools (72.1-5+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libsepol-dev:amd64 (3.7-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgc1:amd64 (1:8.2.8-1) ... Setting up libltdl7:amd64 (2.4.7-8) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-11) ... Setting up libraw23t64:amd64 (0.21.3-1+b1) ... Setting up libboost-atomic1.83-dev:amd64 (1.83.0-4) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up libpcre2-posix3:amd64 (10.44-5) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:amd64 (1.5.0-1+b1) ... Setting up liblqr-1-0:amd64 (0.4.2-2.1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up bison (2:3.8.2+dfsg-1+b2) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up fonts-lmodern (2.005-1) ... Setting up liblua5.4-0:amd64 (5.4.7-1+b1) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.2-1) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-system1.83-dev:amd64 (1.83.0-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libcoordgen3:amd64 (3.0.2-1+b2) ... Setting up libde265-0:amd64 (1.0.15-1+b2) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up libinchi1.07 (1.07.1+dfsg-6) ... Setting up libcatch2-dev (3.7.1-0.4) ... Setting up readline-common (8.2-6) ... Setting up libicu-dev:amd64 (72.1-5+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libfmt10:amd64 (10.1.1+ds1-4) ... Setting up libsynctex2:amd64 (2024.20240313.70630+ds-5) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up libpotrace0:amd64 (1.16-2+b2) ... Setting up libmaeparser-dev:amd64 (1.3.1-1+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up postgresql-client-common (267) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libblkid-dev:amd64 (2.40.2-12) ... Setting up libllvm19:amd64 (1:19.1.5-1) ... Setting up catch2 (3.7.1-0.4) ... Setting up libz3-dev:amd64 (4.13.3-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up flex (2.6.4-8.2+b3) ... Setting up libinchi-dev (1.07.1+dfsg-6) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libncurses-dev:amd64 (6.5-2+b1) ... Setting up gettext (0.22.5-3) ... Setting up libclang1-19 (1:19.1.5-1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up libboost-chrono1.83-dev:amd64 (1.83.0-4) ... Setting up libxpm4:amd64 (1:3.5.17-1+b2) ... Setting up libpcre2-dev:amd64 (10.44-5) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b3) ... Setting up libice-dev:amd64 (2:1.1.1-1) ... Setting up libtool (2.4.7-8) ... Setting up libgirepository-2.0-0:amd64 (2.82.4-1) ... Setting up libselinux1-dev:amd64 (3.7-3+b1) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libboost-system-dev:amd64 (1.83.0.2+b2) ... Setting up libpng-dev:amd64 (1.6.44-3) ... Setting up libcommons-parent-java (56-1) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-4) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libglib2.0-bin (2.82.4-1) ... Setting up libobjc4:amd64 (14.2.0-11) ... Setting up libobjc-14-dev:amd64 (14.2.0-11) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libxdmcp-dev:amd64 (1:1.1.5-1) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-5) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up ssl-cert (1.1.3) ... Setting up libboost-date-time1.83-dev:amd64 (1.83.0-4) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up shared-mime-info (2.4-5+b1) ... Setting up libboost-numpy-dev (1.83.0.2+b2) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-4) ... Setting up ucf (3.0045) ... Setting up libjs-sphinxdoc (8.1.3-2) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.1.0-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Setting up llvm-19-linker-tools (1:19.1.5-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libcoordgen-dev:amd64 (3.0.2-1+b2) ... Setting up llvm-19-runtime (1:19.1.5-1) ... Setting up libboost-regex-dev:amd64 (1.83.0.2+b2) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libmount-dev:amd64 (2.40.2-12) ... Setting up libclang-cpp19 (1:19.1.5-1) ... Setting up libboost-thread1.83-dev:amd64 (1.83.0-4) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libgio-2.0-dev:amd64 (2.82.4-1) ... Setting up girepository-tools:amd64 (2.82.4-1) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libsm-dev:amd64 (2:1.2.4-1) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libpq5:amd64 (17.2-1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up libpq-dev (17.2-1) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up clang-19 (1:19.1.5-1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libfreetype-dev:amd64 (2.13.3+dfsg-1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxcb-shm0-dev:amd64 (1.17.0-2+b1) ... Setting up doxygen (1.9.8+ds-2+b3) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up sphinx-common (8.1.3-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up postgresql-common (267) ... Creating config file /etc/postgresql-common/createcluster.conf with new version Building PostgreSQL dictionaries from installed myspell/hunspell packages... Removing obsolete dictionary files: invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libxcb-render0-dev:amd64 (1.17.0-2+b1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up cmake (3.31.2-1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up llvm-19 (1:19.1.5-1) ... Setting up libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b3) ... Setting up tex-gyre (20180621-6) ... Setting up libboost-thread-dev:amd64 (1.83.0.2+b2) ... Setting up libpangocairo-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libcairo-script-interpreter2:amd64 (1.18.2-2) ... Setting up libxmu6:amd64 (2:1.1.3-3+b3) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-3) ... Setting up postgresql-client-17 (17.2-1) ... update-alternatives: using /usr/share/postgresql/17/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode Setting up libfontconfig-dev:amd64 (2.15.0-1.1+b1) ... Setting up preview-latex-style (13.2-1) ... Setting up python3.12 (3.12.8-3) ... Setting up debhelper (13.21) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up librsvg2-2:amd64 (2.59.2+dfsg-1) ... Setting up libpython3.12t64:amd64 (3.12.8-3) ... Setting up texlive-binaries (2024.20240313.70630+ds-5) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20241115-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up librsvg2-bin (2.59.2+dfsg-1) ... Setting up python3 (3.12.7-1) ... Setting up libpython3.12-dev:amd64 (3.12.8-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-tz (2024.2-1) ... Setting up python3-pil:amd64 (10.4.0-1+b1) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1.1) ... Setting up python3-packaging (24.2-1) ... Setting up texlive-latex-base (2024.20241115-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-mdurl (0.1.2-1) ... Setting up texlive-latex-recommended (2024.20241115-1) ... Setting up python3-greenlet (3.1.0-1+b1) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.8-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up texlive-pictures (2024.20241115-1) ... Setting up python3-urllib3 (2.2.3-4) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-markdown-it (3.0.0-2) ... Setting up texlive-fonts-recommended (2024.20241115-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-commonmark (0.9.1-7) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libgio-2.0-dev-bin (2.82.4-1) ... Setting up libpython3-dev:amd64 (3.12.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-mdit-py-plugins (0.4.2-1) ... Setting up latexmk (1:4.85-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up texlive-latex-extra (2024.20241115-1) ... Setting up python3-sqlalchemy (2.0.32+ds1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.7-1) ... Setting up libboost-python1.83-dev (1.83.0-4) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up libglib2.0-dev-bin (2.82.4-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up libglib2.0-dev:amd64 (2.82.4-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up libcairo2-dev:amd64 (1.18.2-2) ... Setting up llvm-19-tools (1:19.1.5-1) ... Setting up dh-python (6.20241217) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up llvm-19-dev (1:19.1.5-1) ... Setting up postgresql-server-dev-17 (17.2-1) ... Setting up postgresql-server-dev-all:amd64 (267) ... Setting up libheif-plugin-dav1d:amd64 (1.19.3-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.3-1) ... Setting up libheif1:amd64 (1.19.3-1) ... Setting up libmagickcore-7.q16-10:amd64 (8:7.1.1.39+dfsg1-3) ... Setting up libmagickwand-7.q16-10:amd64 (8:7.1.1.39+dfsg1-3) ... Setting up imagemagick-7.q16 (8:7.1.1.39+dfsg1-3) ... update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) doesn't exist update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) doesn't exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) doesn't exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) doesn't exist Setting up imagemagick (8:7.1.1.39+dfsg1-3) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-2) ... Setting up python3-myst-parser (4.0.0-1) ... Setting up python3-recommonmark (0.7.1+ds-5) ... /usr/lib/python3/dist-packages/recommonmark/transform.py:254: SyntaxWarning: invalid escape sequence '\w' match = re.search('[ ]?[\w_-]+::.*', language) Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/rdkit-202409.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202409.2-2_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202409.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael Banck dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean pg_buildext checkcontrol dh clean --with python3 --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' find /build/reproducible-path/rdkit-202409.2 -name "*.pyc" | xargs rm -f rm -f -r Projects/DbCLI/testData/bzr/ rdkit/Chem/inchi.py rm -f -r Docs/Book/_build Code/docs rdkit/docs Code/doxygen_sqlite3.db rm -f \ Code/ForceField/MMFF/test_data/MMFF94_dative_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_dative_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_reference.log \ Code/ForceField/MMFF/test_data/MMFF94s_reference.log \ Code/ForceField/MMFF/test_data/testMMFFForceField.log \ Code/GraphMol/Depictor/test_data/cis_trans_cpp.out.sdf \ Code/GraphMol/Depictor/test_data/collisions.out.sdf \ Code/GraphMol/Depictor/test_data/first_200.out.sdf \ Code/GraphMol/Depictor/test_data/test1.out.sdf \ Code/GraphMol/FileParsers/test_data/blah.sdf \ Code/GraphMol/FileParsers/test_data/cdk2_stereo.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.tdt \ Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf \ Code/GraphMol/FileParsers/test_data/outSmiles.csv \ Code/GraphMol/ForceFieldHelpers/UFF/test_data/Issue62.sdf \ Code/GraphMol/MolAlign/test_data/ref_e2_pyCrippenO3A.sdf \ Code/GraphMol/SLNParse/lex.yysln.cpp \ Code/GraphMol/SLNParse/sln.tab.cpp \ Code/GraphMol/SLNParse/sln.tab.hpp \ Code/GraphMol/SmilesParse/lex.yysmarts.cpp \ Code/GraphMol/SmilesParse/lex.yysmiles.cpp \ Code/GraphMol/SmilesParse/smarts.tab.cpp \ Code/GraphMol/SmilesParse/smarts.tab.hpp \ Code/GraphMol/SmilesParse/smiles.tab.cpp \ Code/GraphMol/SmilesParse/smiles.tab.hpp \ Code/GraphMol/Wrap/test_data/outNCI_few.sdf \ Code/GraphMol/Wrap/test_data/outSmiles.txt \ Code/RDGeneral/versions.cpp \ Docs/Book/Cartridge.rst \ Docs/Book/Install.rst \ Docs/Book/Overview.rst \ rdkit/ML/Data/test_data/testgeneral.dat.pkl \ rdkit/ML/Data/test_data/testquant.qdat.pkl rm -f Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps dh_auto_clean rm -f -rf /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-* make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --with python3 --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_auto_configure -- -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DRDK_BUILD_PGSQL=ON -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_CONFIG=/usr/bin/pg_config -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/17/server" -DPYTHON_EXECUTABLE=/usr/bin/python3.12 ../ cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DRDK_BUILD_PGSQL=ON -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_CONFIG=/usr/bin/pg_config -DPostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql/17/server -DPYTHON_EXECUTABLE=/usr/bin/python3.12 ../ .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Inchi: /usr/lib/x86_64-linux-gnu/libinchi.so -- Found Python3: /usr/bin/python3 (found version "3.12.8") found components: Interpreter Development.Module NumPy Python Install directory /usr/lib/python3.12/site-packages nbval not found, disabling the jupyter tests -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found PostgreSQL: /usr/lib/x86_64-linux-gnu/libpq.so (found version "17.2") == Using strict rotor definition CMake Warning (dev) at External/INCHI-API/CMakeLists.txt:98 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/x86_64-linux-gnu/libmaeparser.so' -- coordgen include dir set as /usr/include -- coordgen libraries set as '/usr/lib/x86_64-linux-gnu/libcoordgen.so' -- Found Python3: /usr/bin/python3 (found version "3.12.8") found components: Interpreter -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/x86_64-linux-gnu/libfreetype.so (found version "2.13.3") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server -- Configuring done (3.1s) -- Generating done (1.9s) CMake Warning: Manually-specified variables were not used by the project: Boost_NO_BOOST_CMAKE CATCH_DIR CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED PYTHON_EXECUTABLE -- Build files have been written to: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu for v in $(pg_buildext supported-versions); do \ (mkdir -p Code/PgSQL/rdkit/build-$v && cd Code/PgSQL/rdkit/build-$v && cmake -DPostgreSQL_CONFIG=/usr/lib/postgresql/$v/bin/pg_config -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/$v/server" -DCMAKE_VERBOSE_MAKEFILE=1 -DRDKit_CodeDir=../../../Code ../); \ done -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PostgreSQL: /usr/lib/x86_64-linux-gnu/libpq.so (found version "17.2") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server -- Configuring done (1.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_auto_build cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.2 -B/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f 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/build/reproducible-path/rdkit-202409.2/External/GA/util/RandomUtil.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o [ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o [ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/LocaleSwitcher.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDLog.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/versions.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh/hc.c [ 1%] Built target inchi_support cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh/hcdriver.c [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/testRDValue.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitVect.cpp [ 4%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Catalogs/Catalog.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o [ 5%] Building CXX object 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/SparseBitVect.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogEntry.cpp [ 5%] Built target testConcurrentQueue /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/EigenSolvers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 5%] Built target EigenSolvers [ 5%] Linking CXX executable logTestsCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 [ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 5%] Built target logTestsCatch /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2024.09.2 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 5%] Built target Catalogs [ 5%] Linking CXX executable testMatrices cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 [ 5%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 5%] Built target testMatrices /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2024.09.2 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2024.09.2 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/testPickers.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2024.09.2 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.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 6%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/catchDataStructs.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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build [ 6%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o [ 6%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/testMultiFPB.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 7%] Built target testQuery /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp [ 9%] Linking CXX executable testRDValue cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDValue.dir/link.d 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CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so [ 9%] Built target testRDValue make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ML/Data /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 9%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB 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Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Data/cQuantize.cpp [ 9%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Atom.cpp [ 9%] Linking CXX executable pickersTestsCatch cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickersTestsCatch.dir/link.d CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 9%] Built target pickersTestsCatch make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make 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Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/AlignPoints.cpp [ 9%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/testTransforms.cpp [ 9%] Linking CXX executable testMultiFPB cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 [ 9%] Linking CXX executable testFPB cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/testGrid.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultiFPB.dir/link.d CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 9%] Built target testMultiFPB make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 9%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/catch_tests.cpp make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 9%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap/Point.cpp /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:193:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 193 | python::def("BulkDiceSimilarity", &BulkDice>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | "return the Dice similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:222:26: required from here 222 | wrapOne("IntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:203:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 203 | python::def("BulkTanimotoSimilarity", | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | &BulkTanimoto>, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 207 | "return the Tanimoto similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 208 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:222:26: required from here 222 | wrapOne("IntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 90 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:214:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 214 | python::def("BulkTverskySimilarity", &BulkTversky>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | (python::args("v1"), python::args("v2"), python::args("a"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 216 | python::args("b"), python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 | "return the Tversky similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:222:26: required from here 222 | wrapOne("IntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:104:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 104 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:193:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long int]' 193 | python::def("BulkDiceSimilarity", &BulkDice>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | "return the Dice similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:223:28: required from here 223 | wrapOne("LongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:203:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long int]' 203 | python::def("BulkTanimotoSimilarity", | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | &BulkTanimoto>, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 207 | "return the Tanimoto similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 208 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:223:28: required from here 223 | wrapOne("LongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 90 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:214:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long int]' 214 | python::def("BulkTverskySimilarity", &BulkTversky>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | (python::args("v1"), python::args("v2"), python::args("a"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 216 | python::args("b"), python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 | "return the Tversky similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:223:28: required from here 223 | wrapOne("LongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:104:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 104 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:193:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' 193 | python::def("BulkDiceSimilarity", &BulkDice>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | "return the Dice similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:224:27: required from here 224 | wrapOne("UIntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:203:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' 203 | python::def("BulkTanimotoSimilarity", | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | &BulkTanimoto>, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 207 | "return the Tanimoto similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 208 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:224:27: required from here 224 | wrapOne("UIntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 90 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:214:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' 214 | python::def("BulkTverskySimilarity", &BulkTversky>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | (python::args("v1"), python::args("v2"), python::args("a"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 216 | python::args("b"), python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 | "return the Tversky similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:224:27: required from here 224 | wrapOne("UIntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:104:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 104 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:193:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long unsigned int]' 193 | python::def("BulkDiceSimilarity", &BulkDice>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | "return the Dice similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:225:29: required from here 225 | wrapOne("ULongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:203:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long unsigned int]' 203 | python::def("BulkTanimotoSimilarity", | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | &BulkTanimoto>, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 206 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 207 | "return the Tanimoto similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 208 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:225:29: required from here 225 | wrapOne("ULongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 90 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:214:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long unsigned int]' 214 | python::def("BulkTverskySimilarity", &BulkTversky>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | (python::args("v1"), python::args("v2"), python::args("a"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 216 | python::args("b"), python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 | "return the Tversky similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:225:29: required from here 225 | wrapOne("ULongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:104:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 104 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ [ 9%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryAtom.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2024.09.2 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so [ 9%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 9%] Built target Alignment make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 10%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Numerics/testConrec.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMetricMatrixCalc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 10%] Built target rdMetricMatrixCalc make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 10%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap/UniformGrid3D.cpp [ 10%] Linking CXX executable testTransforms cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTransforms.dir/link.d CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 10%] Built target testTransforms make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 11%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/c++ 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/AtomIterators.cpp [ 14%] Built target testChemicalFeatures [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/BondIterators.cpp [ 14%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -MF CMakeFiles/GraphMol.dir/Aromaticity.cpp.o.d -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Aromaticity.cpp [ 14%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 [ 14%] Built target rdAlignment [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Kekulize.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ConjugHybrid.cpp [ 14%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKithc.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/AddHs.cpp [ 14%] Built target rdSimDivPickers [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Matrices.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Chirality.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RingInfo.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Conformer.cpp [ 15%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 15%] Built target rdGeometry [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Resonance.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StereoGroup.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/new_canon.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstanceGroup.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MonomerInfo.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FindStereo.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/NontetrahedralStereo.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.cpp.o -MF CMakeFiles/GraphMol.dir/Atropisomers.cpp.o.d -o CMakeFiles/GraphMol.dir/Atropisomers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Atropisomers.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/WedgeBonds.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o -MF CMakeFiles/GraphMol.dir/MolProps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolProps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProps.cpp [ 16%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cDataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 16%] Built target cDataStructs [ 16%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GraphMol.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2024.09.2 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o 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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.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-202409.2/obj-x86_64-linux-gnu' cd 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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'/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make 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Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory/Trajectory.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/MolTransforms.cpp [ 17%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o [ 17%] Building CXX 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPMol.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/External/rapidjson-1.1.0/include -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection 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Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/Trajectory.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPLabeler.cpp [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmartsWrite.cpp [ 21%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2024.09.2 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2024.09.2 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 21%] Built target MolCatalog make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make 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-isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Numerics/Optimizer/LinearSearch.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202409.2/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 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 22%] Built target Subgraphs make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Mancude.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2024.09.2 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2024.09.2 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Numerics/Optimizer/testOptimizer.cpp [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -MF CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o.d -o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Digraph.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 [ 23%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 23%] Built target MolTransforms make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ForceField /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/ForceField.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so [ 23%] Linking CXX executable testOptimizer cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 23%] Built target GenericGroups make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/smiles.tab.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 24%] Built target rdBase [ 24%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 24%] Built target rdChemicalFeatures [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include 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CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraint.cpp [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructUtils.cpp [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2024.09.2 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 24%] Built target ShapeHelpers make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraint.cpp [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.cpp [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/PositionConstraint.cpp [ 24%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 [ 24%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o [ 24%] Built target rdqueries cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp [ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so [ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/TorsionConstraint.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 25%] Built target MolInterchange [ 25%] Built target rdMolCatalog [ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/TorsionAngle.cpp [ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Utils.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Utils.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/AngleBend.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/BondStretch.cpp [ 27%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/StretchBend.cpp [ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/OopBend.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2024.09.2 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2024.09.2 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule5.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 28%] 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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 28%] Built target rdMolTransforms [ 28%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/TorsionAngle.cpp [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Nonbonded.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Params.cpp [ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 [ 28%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SmilesParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 28%] Built target SmilesParse make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make 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"Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build make[4]: 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o [ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o [ 28%] Building CXX object Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/memtest1.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/cptest.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/test2.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o [ 29%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o [ 29%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o [ 29%] Building CXX object Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o [ 29%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o [ 29%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o [ 29%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o [ 29%] Building CXX object Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o cd 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-I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -MF CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o.d -o CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/catch_molops.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 29%] Built target SubstructMatch make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Fingerprints.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 29%] Built target rdMolInterchange make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/smatest.cpp [ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp [ 30%] Linking CXX shared library ../../lib/libRDKitForceField.so cd 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../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 30%] Built target ForceField make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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-fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp [ 30%] Linking CXX executable testPartialCharges cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 [ 30%] Linking CXX executable smiTest2 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest2.dir/link.d CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 30%] Linking CXX executable queryTestsCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 [ 30%] Built target smiTest2 make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp [ 31%] Built target v2smiTestCatch [ 31%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatGenerator.cpp [ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/PatternFingerprints.cpp [ 32%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 32%] 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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 32%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/RDDepictor.cpp [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganFingerprints.cpp [ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 [ 34%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp [ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.cpp [ 34%] Built target rdCIPLabeler make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/CoordGen/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake "--color=" [ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/CoordGen/Wrap/rdCoordGen.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/test1.cpp make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp [ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatParams.cpp [ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragFPGenerator.cpp [ 35%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.2 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl [ 35%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.2 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 35%] Built target MolChemicalFeatures [ 35%] Linking CXX executable graphmolqueryTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 [ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c 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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2024.09.2 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolqueryTest.dir/link.d 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../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 36%] Built target testReducedGraphs [ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp [ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 36%] Built target ForceFieldHelpers make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ForceField /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/catch_tests.cpp make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DistGeom 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/build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistGeomUtils.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2024.09.2 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 36%] 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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 36%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/Wrap/ForceField.cpp [ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintUtil.cpp [ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 [ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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/usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 36%] Built target rdReducedGraphs make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp [ 36%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 36%] Built target rdCoordGen [ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 36%] Linking CXX executable testSLNParse cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 [ 36%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd 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/build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContrib.cpp [ 36%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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/build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContribs.cpp [ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp [ 36%] Linking CXX executable ForceFieldsCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 [ 36%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ForceFieldsCatch.dir/link.d CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -o ForceFieldsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContribs.cpp [ 36%] Linking CXX executable forceFieldHelpersCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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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36%] Built target forceFieldHelpersCatch [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 36%] Built target rdAbbreviations [ 37%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2024.09.2 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 37%] Built target Fingerprints make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make 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-DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 38%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp [ 38%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.2 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 38%] Built target DistGeometry make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DistGeom /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 38%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/testDistGeom.cpp [ 38%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o [ 38%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap/DistGeom.cpp [ 38%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o [ 38%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 38%] Built target rdMolChemicalFeatures [ 38%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2024.09.2 CMakeFiles/Depictor.dir/RDDepictor.cpp.o 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CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp [ 39%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 39%] Built target FilterCatalog make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 40%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 40%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp [ 40%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 40%] Built target rdForceFieldHelpers [ 40%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 40%] Built target testDistGeom [ 40%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 40%] Built target rdForceField [ 40%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 40%] Built target DistGeom [ 40%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2024.09.2 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 40%] Built target MolHash make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 40%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 41%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 41%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 [ 41%] Built target DistGeomHelpers /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDInchiLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2024.09.2 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2024.09.2 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 41%] Built target RDInchiLib make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 42%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdinchi_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -MF CMakeFiles/rdinchi.dir/pyInchi.cpp.o.d -o CMakeFiles/rdinchi.dir/pyInchi.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/INCHI-API/Wrap/pyInchi.cpp [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 42%] Built target rdDepictor [ 42%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 42%] Built target ChemTransforms make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/TplFileParser.cpp [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 44%] Built target rdinchi [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/PDBWriter.cpp [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 44%] Built target rdFingerprintGenerator [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 45%] Built target rdfiltercatalog [ 46%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FileParsers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2024.09.2 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 46%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" make -f 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/build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color=" make -f 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Leaving 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/molopstest.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/testPickler.cpp [ 48%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/test1.cpp [ 48%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/CoordGen/test.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/catch_tests.cpp [ 49%] Linking CXX executable molBundleTest cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp [ 50%] Linking CXX executable graphmolSGroupCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/test1.cpp [ 50%] Linking CXX executable hanoiTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 [ 50%] Linking CXX executable pickleTestsCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target hanoiTest make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickleTestsCatch.dir/link.d CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target pickleTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o.d -o CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -MF CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o.d -o CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testAtropisomers.cpp [ 50%] Linking CXX executable testUFFForceField cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testMolSupplier.cpp [ 50%] Linking CXX executable graphmolAdjustQueryCatch cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolAdjustQueryCatch.dir/link.d CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target graphmolAdjustQueryCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testGeneralFileReader.cpp [ 50%] Linking CXX executable canonTestsCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/canonTestsCatch.dir/link.d CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target canonTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd 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Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp [ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/MDLParser.cpp [ 50%] Linking CXX executable testSGroup cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSGroup.dir/link.d CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2024.09.2 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testMolWriter.cpp [ 50%] Linking CXX executable testSquiggleDoubleBonds cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.dir/link.txt --verbose=1 [ 50%] Linking CXX executable nontetrahedralCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSquiggleDoubleBonds.dir/link.d CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -o testSquiggleDoubleBonds ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 50%] Linking CXX executable testAtropisomers cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAtropisomers.dir/link.d 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target testAtropisomers make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testSequence.cpp [ 50%] Linking CXX executable graphmolTest1 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 [ 50%] Linking CXX executable testMMFFForceField cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTest1.dir/link.d CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 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Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceField.dir/link.d CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target testMMFFForceField make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/file_parsers_catch.cpp [ 50%] Linking CXX executable testSequence cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSequence.dir/link.d CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testPropertyLists.cpp [ 50%] Linking CXX executable testGeneralFileReader [ 50%] Linking CXX executable testMultithreadedMolSupplier cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 [ 50%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp [ 50%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp [ 50%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDepictor.dir/link.d CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target testDepictor make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build [ 50%] Linking CXX executable graphmoltestPickler make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/connectTheDots_catch.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target graphmoltestPickler make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp [ 50%] Linking CXX executable testTplParser cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp [ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 50%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 50%] Built target graphmoltestChirality make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp [ 51%] Linking CXX executable connectTheDotsTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 51%] Built target connectTheDotsTest make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/catch_tests.cpp /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp: In function 'void testMostSubstitutedCoreMatch()': /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1901:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(orthoMeta.std::unique_ptr::get(), 0)' 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1901:60: note: the temporary was destroyed at the end of the full expression 'std::make_pair(ortho.std::unique_ptr::get(), 1)' 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1902:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(meta.std::unique_ptr::get(), 1)' 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1902:55: note: the temporary was destroyed at the end of the full expression 'std::make_pair(biphenyl.std::unique_ptr::get(), 2)' 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(phenyl.std::unique_ptr::get(), 3)' 1903 | std::make_pair(phenyl.get(), 3u)}) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ [ 51%] Linking CXX executable v2FileParsersCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 [ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionPickler.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 51%] Built target v2FileParsersCatchTest 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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/testChemTransforms.cpp [ 51%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 [ 51%] Linking CXX executable v2MolSuppliers cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 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Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 51%] Building CXX object 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 51%] Linking CXX executable multithreadedSupplierCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o -MF CMakeFiles/Descriptors.dir/Crippen.cpp.o.d -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Crippen.cpp [ 52%] Linking CXX executable testMolSupplier cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 [ 52%] Linking CXX executable molfileStereoCatchTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 [ 52%] Built target testMolSupplier 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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints 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../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 52%] Built target molfileStereoCatchTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp [ 52%] Linking CXX executable cdxmlParserCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong 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../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 52%] Built target cdxmlParserCatchTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp [ 52%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 52%] Linking CXX executable testPropertyLists cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPropertyLists.dir/link.d CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 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Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/test1.cpp [ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.cpp [ 54%] Linking CXX executable filterCatalogTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 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Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/catch_tests.cpp [ 54%] Linking CXX executable graphmolTestsCatch cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 54%] Linking CXX executable smiTestCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script 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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.2 ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 54%] Built target chiralityTestsCatch make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 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-c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp [ 54%] Linking CXX executable substructTestCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 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Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 54%] Linking CXX executable testSubstructMatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 54%] Built target testSubstructMatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/catch_tests.cpp [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionDepict.cpp [ 55%] Linking CXX executable molTransformsTestCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTransformsTestCatch.dir/link.d CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -o molTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 55%] Built target molTransformsTestCatch make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp [ 56%] Linking CXX executable testMolTransforms cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolTransforms.dir/link.d 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Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 56%] Built target testMolTransforms make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" [ 56%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testMolAlign.cpp [ 56%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 56%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/catch_tests.cpp [ 56%] Linking CXX executable fpGenTestCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 [ 56%] Linking CXX executable testCrystalForceField cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 [ 56%] Linking CXX executable chemTransformsTestCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 [ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 57%] Built target testCrystalForceField 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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && 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-ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 60%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake "--color=" [ 60%] Built target testFingerprintGenerators make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testShapeHelpers.dir/link.d CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalMCES.cpp [ 60%] Built target testShapeHelpers make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/catch_tests.cpp [ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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61%] Linking CXX executable fileParsersTest1 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 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Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Seed.cpp [ 61%] Linking CXX executable testUFFForceFieldHelpers cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Lipinski.cpp [ 61%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 [ 61%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryTest.dir/link.d CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 61%] Built target trajectoryTest /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/SanitizeRxn.cpp [ 61%] Built target fileParsersCatchTest [ 61%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 [ 62%] Linking CXX executable distGeomHelpersCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 62%] Built target distGeomHelpersCatch [ 62%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2024.09.2 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 62%] 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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 62%] Linking CXX executable molHashCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molHashCatchTest.dir/link.d CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp [ 62%] Linking CXX executable molInterchangeCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 [ 63%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 63%] Built target molInterchangeCatchTest /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolProcessing.so.1 -o ../../../lib/libRDKitMolProcessing.so.1.2024.09.2 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2024.09.2 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so [ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -MF CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o.d -o CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/processing_tests.cpp [ 63%] Linking CXX executable molInterchangeTest1 cd 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp [ 63%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 63%] Built target molInterchangeTest1 [ 63%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 63%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfragcatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/GETAWAY.cpp [ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp [ 67%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp [ 67%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o 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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 67%] Built target ChemReactions make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make -f 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'/build/reproducible-path/rdkit-202409.2/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/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build make -f 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/MolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Pipeline.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Deprotect.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MolOps.cpp [ 68%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/FMCStest.dir/link.d CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so 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-I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp [ 68%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB 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/usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 69%] Built target testReactionFingerprints make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Wrap 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/AtomSymbol.cpp [ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK 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Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp [ 70%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/RepeatUnit.cpp [ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd 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../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 70%] Built target rdFMCS make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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/usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp [ 70%] Built target deprotectTest make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp [ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Validate.cpp [ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Tautomer.cpp [ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp [ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMol.cpp [ 71%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp [ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 71%] Built target testRascalCluster make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp [ 71%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && 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../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp [ 71%] Built target MarvinParser make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testATF.cpp [ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp [ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp [ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 [ 72%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 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../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 72%] Built target rdRascalMCES make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 72%] Built target MolEnumerator make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testEEM.cpp [ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawShape.cpp [ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 72%] Built target rdDeprotect make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 [ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o [ 72%] Built target testAUTOCORR2D cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp [ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o -MF CMakeFiles/testRDF.dir/testRDF.cpp.o.d -o CMakeFiles/testRDF.dir/testRDF.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testRDF.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalMCES.dir/link.d CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 73%] Built target testRascalMCES make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testMORSE.cpp [ 73%] Linking CXX executable testBCUT cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 In file included from /usr/include/c++/14/vector:62, from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testBCUT.dir/link.d CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 73%] Built target testBCUT make -f 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp [ 75%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextJS.cpp [ 76%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp [ 76%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp [ 76%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 77%] Built target rdmolops make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake "--color=" make[4]: Leaving 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -MF CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o.d -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl [ 78%] Built target testWHIM make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 78%] Linking CXX executable testCoulombMat cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 [ 78%] Built target test3D make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 80%] Built target testCoulombMat make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -MF CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o.d -o CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/testMrvToMol.cpp [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp [ 81%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolStandardize.dir/link.d -Wl,-z,relro 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CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 81%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/TautomerQuery.cpp [ 81%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /build/reproducible-path/rdkit-202409.2/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 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CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 81%] Built target MolDraw2D make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/test1.cpp [ 81%] Linking CXX executable descriptorsTestCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 81%] Built target descriptorsTestCatch make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testNormalize.cpp [ 81%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2024.09.2 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2024.09.2 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 81%] Built target O3AAlign make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/TDTMolSupplier.cpp [ 82%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 82%] Built target rdMolEnumerator make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SmilesMolSupplier.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testCharge.cpp [ 83%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 [ 83%] Linking CXX executable testMrvToMol cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMrvToMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 83%] Built target TautomerQuery make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testTautomer.cpp [ 83%] Linking CXX executable testGenericGroups cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMrvToMol.dir/link.d CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 83%] Built target testMrvToMol make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/test2.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGenericGroups.dir/link.d CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 83%] Built target testGenericGroups make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build [ 83%] Linking CXX executable molNormalizeTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testFragment.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molNormalizeTest.dir/link.d CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 83%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/catch_tests.cpp [ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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Linking CXX executable molStandardizeTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 83%] Built target molStandardizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -MF CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o.d -o CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testPipeline.cpp [ 84%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPLabeler.cpp [ 84%] Linking CXX executable molValidateTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 In file included from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, 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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) | ~~^~ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:18: In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) | ~~^~~ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molValidateTest.dir/link.d CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 84%] 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-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) | ~~^~ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) | ~~^~~ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 84%] Linking CXX executable testMolEnumerator cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 84%] Built target testMolEnumerator make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp [ 85%] Linking CXX executable cxsmilesTest cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cxsmilesTest.dir/link.d CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 85%] Built target cxsmilesTest [ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SmilesWriter.cpp [ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SDWriter.cpp [ 85%] Linking CXX executable molStandardizeSmallTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 85%] Built target molStandardizeSmallTest make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 85%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/catch_tests.cpp [ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 85%] Built target molChargeTest make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Mancude.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp [ 86%] Linking CXX executable molFragmentTest cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp [ 88%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Sort.cpp [ 90%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD 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CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 90%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp [ 90%] Linking CXX executable molTautomerTest cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTautomerTest.dir/link.d CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 90%] Built target molTautomerTest make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp [ 90%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 90%] Built target rdTautomerQuery make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp [ 90%] Linking CXX executable molStandardizePipelineTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizePipelineTest.dir/link.d CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -o molStandardizePipelineTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 90%] Built target molStandardizePipelineTest make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 91%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-x86_64-linux-gnu' [ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp [ 91%] Linking CXX executable molStandardizeCatchTest cd /build/reproducible-path/rdkit-202409.2/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 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Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp [ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule3.cpp [ 92%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 [ 92%] Linking CXX executable moldraw2DRxnTest1 cd /build/reproducible-path/rdkit-202409.2/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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolfiles.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 92%] Built target rdmolfiles [ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 92%] Built target moldraw2DRxnTest1 [ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MolBundle.cpp [ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp [ 93%] Linking CXX executable testScaffoldNetwork cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 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../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 94%] Built target rdScaffoldNetwork make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp [ 94%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit 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-I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_op.c [ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o cd 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-I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/cache.c [ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/guc.c [ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_gist.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_gin.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bitstring.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rdkit_io.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc 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-isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rxn_op.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/sfp_op.c [ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 [ 96%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] Built target moldraw2DTest1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] Built target rdChemReactions /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp:1617:38: warning: unused parameter 'data' [-Wunused-parameter] 1617 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, | ~~~~~~~^~~~ /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp:1617:49: warning: unused parameter 'isQuery' [-Wunused-parameter] 1617 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, | ~~~~~^~~~~~~ /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp:1618:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] 1618 | unsigned int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ [ 96%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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/usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] Built target rdchem [ 96%] Linking CXX executable generalizedSubstructCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] 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/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend make[4]: Entering directory 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../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] Built target rdGeneralizedSubstruct [ 96%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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/usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] Built target rdMolStandardize [ 96%] Linking CXX shared library librdkit.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/sql cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/data 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CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/lib /usr/lib/x86_64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2024.09.2 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] Built target rdkit [ 96%] Linking CXX executable gaExample cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] Built target gaExample [ 97%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 97%] Built target testRGroupDecompInternals [ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 97%] Built target SubstructLibrary make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o [ 98%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/catch_tests.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [ 99%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 99%] Built target rgroupCatchTests [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../../lib/libRDKitga.so.1.2024.09.2 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 99%] Built target rdRGroupDecomposition [100%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [100%] Built target moldraw2DTestCatch [100%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 [100%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [100%] Built target substructLibraryCatchTest /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [100%] Built target substructLibraryTest [100%] Linking CXX executable testRGroupDecomp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [100%] Built target testRGroupDecomp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [100%] Built target rdSubstructLibrary make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' for v in $(pg_buildext supported-versions); do \ (cd Code/PgSQL/rdkit/build-$v && make || $(cat ../../../../obj-*/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/link.txt | sed -e 's#\.\./\.\./#../../../../obj-*/Code/#g')); \ done make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit -B/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17/CMakeFiles /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17' make -f CMakeFiles/rdkit.dir/build.make CMakeFiles/rdkit.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17' cd /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17 /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17 /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17' make -f CMakeFiles/rdkit.dir/build.make CMakeFiles/rdkit.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17' [ 7%] Building CXX object CMakeFiles/rdkit.dir/adapter.cpp.o /usr/bin/c++ -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp [ 14%] Building C object CMakeFiles/rdkit.dir/bfp_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_op.c [ 21%] Building C object CMakeFiles/rdkit.dir/cache.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/cache.c [ 28%] Building C object CMakeFiles/rdkit.dir/guc.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/guc.c [ 35%] Building C object CMakeFiles/rdkit.dir/low_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/low_gist.c [ 42%] Building C object CMakeFiles/rdkit.dir/mol_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/mol_op.c [ 50%] Building C object CMakeFiles/rdkit.dir/rdkit_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rdkit_gist.c [ 57%] Building C object CMakeFiles/rdkit.dir/bfp_gist.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_gist.c [ 64%] Building C object CMakeFiles/rdkit.dir/bfp_gin.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_gin.c [ 71%] Building C object CMakeFiles/rdkit.dir/bitstring.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bitstring.c [ 78%] Building C object CMakeFiles/rdkit.dir/rdkit_io.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rdkit_io.c [ 85%] Building C object CMakeFiles/rdkit.dir/rxn_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rxn_op.c [ 92%] Building C object CMakeFiles/rdkit.dir/sfp_op.c.o /usr/bin/cc -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/../../../Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/sfp_op.c [100%] Linking CXX shared library librdkit.so /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17/sql /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17/data /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17/expected /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 /usr/bin/ld: cannot find -lGeneralizedSubstruct: No such file or directory /usr/bin/ld: cannot find -lMolEnumerator: No such file or directory /usr/bin/ld: cannot find -lTautomerQuery: No such file or directory /usr/bin/ld: cannot find -lMolDraw2D: No such file or directory /usr/bin/ld: cannot find -lMolTransforms: No such file or directory /usr/bin/ld: cannot find -lMolHash: No such file or directory /usr/bin/ld: cannot find -lFMCS: No such file or directory /usr/bin/ld: cannot find -lChemReactions: No such file or directory /usr/bin/ld: cannot find -lChemTransforms: No such file or directory /usr/bin/ld: cannot find -lFileParsers: No such file or directory /usr/bin/ld: cannot find -lSmilesParse: No such file or directory /usr/bin/ld: cannot find -lFingerprints: No such file or directory /usr/bin/ld: cannot find -lSubgraphs: No such file or directory /usr/bin/ld: cannot find -lDescriptors: No such file or directory /usr/bin/ld: cannot find -lPartialCharges: No such file or directory /usr/bin/ld: cannot find -lSubstructMatch: No such file or directory /usr/bin/ld: cannot find -lGraphMol: No such file or directory /usr/bin/ld: cannot find -lEigenSolvers: No such file or directory /usr/bin/ld: cannot find -lDataStructs: No such file or directory /usr/bin/ld: cannot find -lDepictor: No such file or directory /usr/bin/ld: cannot find -lRDGeometryLib: No such file or directory /usr/bin/ld: cannot find -lRDGeneral: No such file or directory /usr/bin/ld: cannot find -lrdkit_base: No such file or directory collect2: error: ld returned 1 exit status /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o 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To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SYMBOL_CACHE_SIZE' at line 337 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 557 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 869 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_TIMESTAMP' at line 965 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_ALIGN_MEMBERS' at line 971 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'USE_INLINE_TREES' at line 1162 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'FORMULA_TRANSPARENT' at line 1189 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1327 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1425 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1431 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1596 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 1608 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1617 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTNAME' at line 1647 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTSIZE' at line 1652 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_TRANSPARENT' at line 1792 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. Doxygen version used: 1.9.8 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... 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for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/tutorial Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DetermineBonds Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt/Demo Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Fonts Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/libs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/RDGeneral Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/hash Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/hash/detail Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ForceField Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics/EigenSolvers Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/Abbreviations.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/Abbreviations.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Atom.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Atom.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/atomic_data.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/atomic_data.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/AtomIterators.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/AtomIterators.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Atropisomers.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Atropisomers.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Bond.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Bond.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/BondIterators.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/BondIterators.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Canon.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Canon.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h../build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionParser.h:171: warning: unbalanced grouping commands . Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/PreprocessRxn.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/PreprocessRxn.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Reaction.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Reaction.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionParser.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionParser.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionPickler.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionPickler.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionRunner.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionRunner.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/SanitizeRxn.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/SanitizeRxn.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/ChemTransforms.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/ChemTransforms.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/MolFragmenter.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/MolFragmenter.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Chirality.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Chirality.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPLabeler.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPLabeler.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPMol.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPMol.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Configuration.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Configuration.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Descriptor.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Descriptor.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Digraph.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Digraph.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Edge.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Edge.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Mancude.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Mancude.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Node.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Node.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Priority.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Priority.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule2.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule2.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule3.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule3.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule5.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule5.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule6.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule6.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rules.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rules.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Sort.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Sort.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Conformer.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Conformer.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/DepictUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/DepictUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/EmbeddedFrag.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/EmbeddedFrag.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/RDDepictor.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/RDDepictor.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Templates.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Templates.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/TemplateSmiles.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/TemplateSmiles.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Deprotect.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Deprotect.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/AtomFeat.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/AtomFeat.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/AUTOCORR2D.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/AUTOCORR2D.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/AUTOCORR3D.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/AUTOCORR3D.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/CoulombMat.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/CoulombMat.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Crippen.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/DCLV.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/DCLV.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/EEM.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/EEM.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/OxidationNumbers.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/OxidationNumbers.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Property.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/details.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/details.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DetermineBonds/DetermineBonds.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DetermineBonds/DetermineBonds.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/CDXMLParser.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/CDXMLParser.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/GeneralFileReader.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/GeneralFileReader.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MaestroProperties.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MaestroProperties.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSGroupParsing.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSGroupParsing.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSGroupWriting.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSGroupWriting.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.v1API.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.v1API.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/PNGParser.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/PNGParser.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MHFP.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MHFP.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Graph.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Seed.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Target.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Target.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GenericGroups/GenericGroups.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GenericGroups/GenericGroups.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GraphMol.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GraphMol.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinDefs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinDefs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinParser.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinParser.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolBundle.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolBundle.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/AtomSymbol.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/AtomSymbol.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMol.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMol.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawShape.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawShape.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFT.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFT.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Parsing file /buil/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h:233: warning: unbalanced grouping commands d/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextJS.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextJS.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/StringRect.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/StringRect.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/LinkNode.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/LinkNode.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/mf.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/mf.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash//build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolOps.h:489: warning: unbalanced grouping commands /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolOps.h:747: warning: unbalanced grouping commands MolHash.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/nmmolhash.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/nmmolhash.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/details.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolOps.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolOps.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolPickler.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolPickler.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/MolProcessing.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/MolProcessing.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Pipeline.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Pipeline.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MonomerInfo.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MonomerInfo.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/new_canon.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/new_canon.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PeriodicTable.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PeriodicTable.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryAtom.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryAtom.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryBond.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryBond.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/PartitionSet.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/PartitionSet.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalDetails.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalDetails.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalMCES.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalMCES.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalOptions.h... Parsing file /buil/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ROMol.h:416: warning: unbalanced grouping commands d/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalOptions.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalResult.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalResult.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RDKitBase.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RDKitBase.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RDKitQueries.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RDKitQueries.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Resonance.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Resonance.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupData.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupData.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RingInfo.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RingInfo.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Rings.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Rings.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ROMol.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ROMol.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RWMol.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RWMol.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SanitException.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SanitException.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/detail.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/detail.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/primes.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/primes.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StereoGroup.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StereoGroup.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/StructCheckerOptions.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/StructCheckerOptions.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/Utilites.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstanceGroup.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstanceGroup.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/PatternFactory.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/PatternFactory.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/TautomerQuery.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/TautomerQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Catalogs/Catalog.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Catalogs/Catalog.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogParams.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/base64.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/base64.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitOps.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitOps.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitVect.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitVect.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitVects.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitVects.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitVectUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitVectUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DatastructsException.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DatastructsException.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DatastructsStreamOps.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DatastructsStreamOps.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DiscreteDistMat.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DiscreteDistMat.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DiscreteValueVect.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DiscreteValueVect.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/ExplicitBitVect.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/ExplicitBitVect.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/FPBReader.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/FPBReader.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/MultiFPBReader.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/MultiFPBReader.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/SparseBitVect.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/SparseBitVect.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataStructs/SparseIntVect.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataStructs/SparseIntVect.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Query/AndQuery.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Query/AndQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Query/EqualityQuery.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Query/EqualityQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Query/GreaterEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Query/GreaterEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Query/GreaterQuery.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Query/GreaterQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Query/LessEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Query/LessEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Query/LessQuery.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Query/LessQuery.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Query/NullQueryAlgebra.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Query/NullQueryAlgebra.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Query/OrQuery.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Query/OrQuery.h... 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Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/InfoBitRanker.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/InfoBitRanker.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/InfoGainFuncs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/InfoGainFuncs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/DistPicker.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/DistPicker.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/LeaderPicker.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/LeaderPicker.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/MaxMinPicker.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/BadFileException.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/BadFileException.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/BoostEndInclude.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/BoostEndInclude.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/BoostStartInclude.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/BoostStartInclude.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/ConcurrentQueue.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/ConcurrentQueue.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Dict.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Dict.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Exceptions.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Exceptions.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/export.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/export.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/FileParseException.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/FileParseException.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/hanoiSort.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/hanoiSort.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Invariant.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Invariant.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/LocaleSwitcher.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Ranking.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Ranking.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDAny.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDAny.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDConfig.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDConfig.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDExportMacros.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDExportMacros.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDLog.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDLog.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDProps.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDProps.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDThreads.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDThreads.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDValue.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDValue.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/StreamOps.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/StreamOps.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/types.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/types.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/utils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/utils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/versions.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/versions.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDBoost/boost_numpy.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDBoost/boost_numpy.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDBoost/import_array.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDBoost/import_array.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDBoost/pyint_api.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDBoost/pyint_api.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/BoundsMatrix.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/BoundsMatrix.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralSet.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralSet.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContrib.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContrib.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContribs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContribs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistGeomUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistGeomUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContrib.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContrib.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContribs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContribs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/FourthDimContrib.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/FourthDimContrib.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/FourthDimContribs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/FourthDimContribs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/DistGeom/TriangleSmooth.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/DistGeom/TriangleSmooth.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/Contrib.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/Contrib.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/ForceField.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/ForceField.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/OopBend.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/OopBend.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Params.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Inversion.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Inversion.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Inversions.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Inversions.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Params.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Utils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Utils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Numerics/Conrec.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Numerics/Conrec.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Numerics/Matrix.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Numerics/Matrix.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Numerics/SquareMatrix.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Numerics/SquareMatrix.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Numerics/SymmMatrix.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Numerics/SymmMatrix.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Numerics/Vector.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Numerics/Vector.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Geometry/Grid3D.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Geometry/Grid3D.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Geometry/GridUtils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Geometry/GridUtils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Geometry/point.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Geometry/point.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Geometry/Transform.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Geometry/Transform.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Geometry/Transform2D.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Geometry/Transform2D.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Geometry/Transform3D.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Geometry/Transform3D.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Geometry/UniformGrid3D.h... Parsing file /build/reproducible-pat/build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:62: warning: documented symbol 'for experimental torsion angle RDKit::DGeomHelpers::preferences' was not declared or defined. /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolOps.h:1187: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolOps.h:1203: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Pipeline.h:90: warning: documented symbol 'enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::PipelineStatus' was not declared or defined. /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:94: warning: no matching file member found for RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON(const std::map &rgr, const std::string &prefix="") Possible candidates: 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRow &rgr, const std::string &prefix="")' at line 82 of file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRows &rgr, const std::string &prefix="")' at line 86 of file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupColumn &rgr, const std::string &prefix="")' at line 90 of file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupUtils.h /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' h/rdkit-202409.2/Code/Geometry/UniformGrid3D.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Geometry/Utils.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Geometry/Utils.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/Features/Feature.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/Features/Feature.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/FreeChemicalFeature.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Catalog.h... Generating code for file CatalogEntry.h... Generating code for file CatalogParams.h... Generating code for file ChemicalFeature.h... Generating code for file FreeChemicalFeature.h... Generating code for file MetricFuncs.h... Generating code for file MetricMatrixCalc.h... Generating code for file base64.h... Generating code for file BitOps.h... Generating code for file BitVect.h... Generating code for file BitVects.h... Generating code for file BitVectUtils.h... Generating code for file DatastructsException.h... Generating code for file DatastructsStreamOps.h... Generating code for file DiscreteDistMat.h... Generating code for file DiscreteValueVect.h... Generating code for file ExplicitBitVect.h... Generating code for file FPBReader.h... Generating code for file MultiFPBReader.h... Generating code for file SparseBitVect.h... Generating code for file SparseIntVect.h... Generating code for file BoundsMatrix.h... Generating code for file ChiralSet.h... Generating code for file ChiralViolationContrib.h... Generating code for file ChiralViolationContribs.h... Generating code for file DistGeomUtils.h... Generating code for file DistViolationContrib.h... Generating code for file DistViolationContribs.h... Generating code for file FourthDimContrib.h... Generating code for file FourthDimContribs.h... Generating code for file TriangleSmooth.h... Generating code for file Feature.h... Generating code for file AngleConstraints.h... Generating code for file Contrib.h... Generating code for file DistanceConstraints.h... Generating code for file ForceField.h... Generating code for file OopBend.h... Generating code for file StretchBend.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... Generating code for file AngleConstraint.h... Generating code for file AngleConstraint.h... Generating code for file BondStretch.h... Generating code for file BondStretch.h... Generating code for file Contribs.h... Generating code for file Contribs.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file Inversion.h... Generating code for file Inversions.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file Utils.h... Generating code for file Utils.h... Generating code for file Grid3D.h... Generating code for file GridUtils.h... Generating code for file point.h... Generating code for file Transform.h... Generating code for file Transform2D.h... Generating code for file Transform3D.h... Generating code for file UniformGrid3D.h... Generating code for file Abbreviations.h... Generating code for file Atom.h... Generating code for file atomic_data.h... Generating code for file AtomIterators.h... Generating code for file Atropisomers.h... Generating code for file Bond.h... Generating code for file BondIterators.h... Generating code for file Canon.h... Generating code for file CartesianProduct.h... Generating code for file Enumerate.h... Generating code for file EnumerateBase.h... Generating code for file EnumerateTypes.h... Generating code for file EnumerationPickler.h... Generating code for file EnumerationStrategyBase.h... Generating code for file EvenSamplePairs.h... Generating code for file RandomSample.h... Generating code for file RandomSampleAllBBs.h... Generating code for file PreprocessRxn.h... Generating code for file Reaction.h... Generating code for file ReactionFingerprints.h... Generating code for file ReactionParser.h... Generating code for file ReactionPickler.h... Generating code for file ReactionRunner.h... Generating code for file ReactionUtils.h... Generating code for file SanitizeRxn.h... Generating code for file ChemTransforms.h... Generating code for file MolFragmenter.h... Generating code for file Chirality.h... Generating code for file CIPLabeler.h... Generating code for file CIPMol.h... Generating code for file AtropisomerBond.h... Generating code for file Configuration.h... Generating code for file Sp2Bond.h... Generating code for file Tetrahedral.h... Generating code for file Descriptor.h... Generating code for file Digraph.h... Generating code for file Edge.h... Generating code for file Mancude.h... Generating code for file Node.h... Generating code for file Priority.h... Generating code for file Pairlist.h... Generating code for file Rule1a.h... Generating code for file Rule1b.h... Generating code for file Rule2.h... Generating code for file Rule3.h... Generating code for file Rule4a.h... Generating code for file Rule4b.h... Generating code for file Rule4c.h... Generating code for file Rule5.h... Generating code for file Rule5New.h... Generating code for file Rule6.h... Generating code for file Rules.h... Generating code for file SequenceRule.h... Generating code for file Sort.h... Generating code for file TooManyNodesException.h... Generating code for file Conformer.h... Generating code for file DepictUtils.h... Generating code for file EmbeddedFrag.h... Generating code for file RDDepictor.h... Generating code for file Templates.h... Generating code for file TemplateSmiles.h... Generating code for file Deprotect.h... Generating code for file AtomFeat.h... Generating code for file AUTOCORR2D.h... Generating code for file AUTOCORR3D.h... Generating code for file BCUT.h... Generating code for file ConnectivityDescriptors.h... Generating code for file CoulombMat.h... Generating code for file Crippen.h... Generating code for file Data3Ddescriptors.h... Generating code for file DCLV.h... Generating code for file EEM.h... Generating code for file GETAWAY.h... Generating code for file Lipinski.h... Generating code for file MolData3Ddescriptors.h... Generating code for file MolDescriptors.h... Generating code for file MolDescriptors3D.h... Generating code for file MolSurf.h... Generating code for file MORSE.h... Generating code for file MQN.h... Generating code for file OxidationNumbers.h... Generating code for file PBF.h... Generating code for file PMI.h... Generating code for file Property.h... Generating code for file RDF.h... Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... Generating code for file CDXMLParser.h... Generating code for file FileParsers.h... Generating code for file FileParserUtils.h... Generating code for file FileWriters.h... Generating code for file GeneralFileReader.h... Generating code for file MaestroProperties.h... Generating code for file MolFileStereochem.h... Generating code for file MolSGroupParsing.h... Generating code for file MolSGroupWriting.h... Generating code for file MolSupplier.h... Generating code for file MolSupplier.v1API.h... Generating code for file MolWriters.h... Generating code for file MultithreadedMolSupplier.h... Generating code for file MultithreadedSDMolSupplier.h... Generating code for file MultithreadedSmilesMolSupplier.h... Generating code for file PNGParser.h... Generating code for file ProximityBonds.h... Generating code for file SequenceParsers.h... Generating code for file SequenceWriters.h... Generating code for file FilterCatalog.h... Generating code for file FilterCatalogEntry.h... Generating code for file FilterMatcherBase.h... Generating code for file FilterMatchers.h... Generating code for file Filters.h... Generating code for file FunctionalGroupHierarchy.h... Generating code for file AtomPairGenerator.h... Generating code for file AtomPairs.h... Generating code for file FingerprintGenerator.h... Generating code for file Fingerprints.h... Generating code for file FingerprintUtil.h... Generating code for file MACCS.h... Generating code for file MHFP.h... Generating code for file MorganFingerprints.h... Generating code for file MorganGenerator.h... Generating code for file RDKitFPGenerator.h... Generating code for file TopologicalTorsionGenerator.h... Generating code for file Composition2N.h... Generating code for file DebugTrace.h... Generating code for file DuplicatedSeedCache.h... Generating code for file FMCS.h... Generating code for file Graph.h... Generating code for file MatchTable.h... Generating code for file MaximumCommonSubgraph.h... Generating code for file Seed.h... Generating code for file SeedSet.h... Generating code for file SubstructMatchCustom.h... Generating code for file SubstructureCache.h... Generating code for file Target.h... Generating code for file TargetMatch.h... Generating code for file TorsionAngleContribs.h... Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... Generating code for file MMFF.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... Generating code for file UFF.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... Generating code for file FragCatGenerator.h... Generating code for file FragCatParams.h... Generating code for file FragFPGenerator.h... Generating code for file XQMol.h... Generating code for file GenericGroups.h... Generating code for file GraphMol.h... Generating code for file MarvinDefs.h... Generating code for file MarvinParser.h... Generating code for file MMPA.h... Generating code for file AlignMolecules.h... Generating code for file O3AAlignMolecules.h... Generating code for file MolBundle.h... Generating code for file MolCatalog.h... Generating code for file MolCatalogEntry.h... Generating code for file MolCatalogParams.h... Generating code for file FeatureParser.h... Generating code for file MolChemicalFeature.h... Generating code for file MolChemicalFeatureDef.h... Generating code for file MolChemicalFeatureFactory.h... Generating code for file AtomSymbol.h... Generating code for file DrawAnnotation.h... Generating code for file DrawMol.h... Generating code for file DrawMolMCH.h... Generating code for file DrawMolMCHCircleAndLine.h... Generating code for file DrawMolMCHLasso.h... Generating code for file DrawShape.h... Generating code for file DrawText.h... Generating code for file DrawTextCairo.h... Generating code for file DrawTextFT.h... Generating code for file DrawTextFTCairo.h... Generating code for file DrawTextFTJS.h... Generating code for file DrawTextFTSVG.h... Generating code for file DrawTextJS.h... Generating code for file DrawTextNotFT.h... Generating code for file DrawTextSVG.h... Generating code for file roboto_regular.h... Generating code for file telex_regular.h... Generating code for file MolDraw2D.h... Generating code for file MolDraw2DCairo.h... Generating code for file MolDraw2DDetails.h... Generating code for file MolDraw2DHelpers.h... Generating code for file MolDraw2DJS.h... Generating code for file MolDraw2DSVG.h... Generating code for file MolDraw2DUtils.h... Generating code for file MolDraw2Dwx.h... Generating code for file DrawTextFTQt.h... Generating code for file DrawTextQt.h... Generating code for file MolDraw2DQt.h... Generating code for file StringRect.h... Generating code for file LinkNode.h... Generating code for file MolEnumerator.h... Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.h... Generating code for file details.h... Generating code for file details.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... Generating code for file MolProcessing.h... Generating code for file AcidBaseCatalogEntry.h... Generating code for file AcidBaseCatalogParams.h... Generating code for file AcidBaseCatalogUtils.h... Generating code for file Charge.h... Generating code for file Fragment.h... Generating code for file FragmentCatalogEntry.h... Generating code for file FragmentCatalogParams.h... Generating code for file FragmentCatalogUtils.h... Generating code for file Metal.h... Generating code for file MolStandardize.h... Generating code for file Normalize.h... Generating code for file Pipeline.h... Generating code for file Tautomer.h... Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... Generating code for file TransformCatalogEntry.h... Generating code for file TransformCatalogParams.h... Generating code for file TransformCatalogUtils.h... Generating code for file Validate.h... Generating code for file MolTransforms.h... Generating code for file MonomerInfo.h... Generating code for file new_canon.h... Generating code for file GasteigerCharges.h... Generating code for file GasteigerParams.h... Generating code for file PeriodicTable.h... Generating code for file QueryAtom.h... Generating code for file QueryBond.h... Generating code for file QueryOps.h... Generating code for file PartitionSet.h... Generating code for file RascalClusterOptions.h... Generating code for file RascalDetails.h... Generating code for file RascalMCES.h... Generating code for file RascalOptions.h... Generating code for file RascalResult.h... Generating code for file RDKitBase.h... Generating code for file RDKitQueries.h... Generating code for file ReducedGraphs.h... Generating code for file Resonance.h... Generating code for file RGroupCore.h... Generating code for file RGroupData.h... Generating code for file RGroupDecomp.h... Generating code for file RGroupDecompData.h... Generating code for file RGroupDecompParams.h... Generating code for file RGroupFingerprintScore.h... Generating code for file RGroupGa.h... Generating code for file RGroupMatch.h... Generating code for file RGroupScore.h... Generating code for file RGroupUtils.h... Generating code for file RingInfo.h... Generating code for file Rings.h... Generating code for file ROMol.h... Generating code for file RWMol.h... Generating code for file SanitException.h... Generating code for file detail.h... Generating code for file ScaffoldNetwork.h... Generating code for file ShapeEncoder.h... Generating code for file ShapeUtils.h... Generating code for file SLNAttribs.h... Generating code for file SLNParse.h... Generating code for file SLNParseOps.h... Generating code for file CanonicalizeStereoGroups.h... Generating code for file primes.h... Generating code for file SmartsWrite.h... Generating code for file SmilesParse.h... Generating code for file SmilesParseOps.h... Generating code for file SmilesWrite.h... Generating code for file StereoGroup.h... Generating code for file Pattern.h... Generating code for file ReCharge.h... Generating code for file Stereo.h... Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... Generating code for file SubstanceGroup.h... Generating code for file SubstructMatch.h... Generating code for file SubstructUtils.h... Generating code for file PatternFactory.h... Generating code for file SubstructLibrary.h... Generating code for file SubstructLibrarySerialization.h... Generating code for file TautomerQuery.h... Generating code for file Snapshot.h... Generating code for file Trajectory.h... Generating code for file CorrMatGenerator.h... Generating code for file InfoBitRanker.h... Generating code for file InfoGainFuncs.h... Generating code for file AlignPoints.h... Generating code for file Conrec.h... Generating code for file PowerEigenSolver.h... Generating code for file Matrix.h... Generating code for file BFGSOpt.h... Generating code for file SquareMatrix.h... Generating code for file SymmMatrix.h... Generating code for file Vector.h... Generating code for file AndQuery.h... Generating code for file EqualityQuery.h... Generating code for file GreaterEqualQuery.h... Generating code for file GreaterQuery.h... Generating code for file LessEqualQuery.h... Generating code for file LessQuery.h... Generating code for file NullQueryAlgebra.h... Generating code for file OrQuery.h... Generating code for file Query.h... Generating code for file QueryObjects.h... Generating code for file RangeQuery.h... Generating code for file SetQuery.h... Generating code for file XOrQuery.h... Generating code for file boost_numpy.h... Generating code for file import_array.h... Generating code for file pyint_api.h... Generating code for file PySequenceHolder.h... Generating code for file python.h... Generating code for file python_streambuf.h... Generating code for file BadFileException.h... Generating code for file BoostEndInclude.h... Generating code for file BoostStartInclude.h... Generating code for file ConcurrentQueue.h... Generating code for file Dict.h... Generating code for file Exceptions.h... Generating code for file export.h... Generating code for file FileParseException.h... Generating code for file hanoiSort.h... Generating code for file Invariant.h... Generating code for file LocaleSwitch/build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitOps.h:188: warning: found at different nesting level (7) than expected (4) /build/reproducible-path/rdkit-202409.2/Code/DataStructs/BitOps.h:189: warning: end of comment block while expecting command er.h... Generating code for file Ranking.h... Generating code for file RDAny.h... Generating code for file RDConfig.h... Generating code for file RDExportMacros.h... Generating code for file RDLog.h... Generating code for file RDProps.h... Generating code for file RDThreads.h... Generating code for file RDValue-doublemagic.h... Generating code for file RDValue-taggedunion.h... Generating code for file RDValue.h... Generating code for file StreamOps.h... Generating code for file types.h... Generating code for file utils.h... Generating code for file versions.h... Generating code for file DistPicker.h... Generating code for file HierarchicalClusterPicker.h... Generating code for file LeaderPicker.h... Generating code for file MaxMinPicker.h... Generating file documentation... Generating docs for file Catalog.h... Generating docs for file CatalogEntry.h... Generating docs for file CatalogParams.h... Generating docs for file ChemicalFeature.h... Generating docs for file FreeChemicalFeature.h... Generating docs for file MetricFuncs.h... Generating docs for file MetricMatrixCalc.h... Generating docs for file base64.h... Generating docs for file BitOps.h... Generating docs for file BitVect.h... Generating docs for file BitVects.h... Generating docs for file BitVectUtils.h... Generating docs for file DatastructsException.h... Generating docs for file DatastructsStreamOps.h... Generating docs for file DiscreteDistMat.h... Generating docs for file DiscreteValueVect.h... Generating docs for file ExplicitBitVect.h... Generating docs for file FPBReader.h... Generating docs for file MultiFPBReader.h... Generating docs for file SparseBitVect.h... Generating docs for file SparseIntVect.h... Generating docs for file BoundsMatrix.h... Generating docs for file ChiralSet.h... Generating docs for file ChiralViolationContrib.h... Generating docs for file ChiralViolationContribs.h... Generating docs for file DistGeomUtils.h... Generating docs for file DistViolationContrib.h... Generating docs for file DistViolationContribs.h... Generating docs for file FourthDimContrib.h... Generating docs for file FourthDimContribs.h... Generating docs for file TriangleSmooth.h... Generating docs for file Feature.h... Generating docs for file AngleConstraints.h... Generating docs for file Contrib.h... Generating docs for file DistanceConstraints.h... Generating docs for file ForceField.h... Generating docs for file OopBend.h... Generating docs for file StretchBend.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraint.h... Generating docs for file BondStretch.h... Generating docs for file BondStretch.h... Generating docs for file Contribs.h... Generating docs for file Contribs.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file Inversion.h... Generating docs for file Inversions.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... Generating docs for file Utils.h... Generating docs for file Utils.h... Generating docs for file Grid3D.h... Generating docs for file GridUtils.h... Generating docs for file point.h... Generating docs for file Transform.h... Generating docs for file Transform2D.h... Generating docs for file Transform3D.h... Generating docs for file UniformGrid3D.h... Generating docs for file Abbreviations.h... Generating docs for file Atom.h... Generating docs for file atomic_data.h... Generating docs for file AtomIterators.h... Generating docs for file Atropisomers.h... Generating docs for file Bond.h... Generating docs for file BondIterators.h... Generating docs for file Canon.h... Generating docs for file CartesianProduct.h... Generating docs for file Enumerate.h... Generating docs for file EnumerateBase.h... Generating docs for file EnumerateTypes.h... Generating docs for file EnumerationPickler.h... Generating docs for file EnumerationStrategyBase.h... Generating docs for file EvenSamplePairs.h... Generating docs for file RandomSample.h... Generating docs for file RandomSampleAllBBs.h... Generating docs for file PreprocessRxn.h... Generating docs for file Reaction.h... Generating docs for file ReactionFingerprints.h... Generating docs for file ReactionParser.h... Generating docs for file ReactionPickler.h... Generating docs for file ReactionRunner.h... Generating docs for file ReactionUtils.h... Generating docs for file SanitizeRxn.h... Generating docs for file ChemTransforms.h... Generating docs for file MolFragmenter.h... Generating docs for file Chirality.h... Generating docs for file CIPLabeler.h... Generating docs for file CIPMol.h... Generating docs for file AtropisomerBond.h... Generating docs for file Configuration.h... Generating docs for file Sp2Bond.h... Generating docs for file Tetrahedral.h... Generating docs for file Descriptor.h... Generating docs for file Digraph.h... Generating docs for file Edge.h... Generating docs for file Mancude.h... Generating docs for file Node.h... Generating docs for file Priority.h... Generating docs for file Pairlist.h... Generating docs for file Rule1a.h... Generating docs for file Rule1b.h... Generating docs for file Rule2.h... Generating docs for file Rule3.h... Generating docs for file Rule4a.h... Generating docs for file Rule4b.h... Generating docs for file Rule4c.h... Generating docs for file Rule5.h... Generating docs for file Rule5New.h... Generating docs for file Rule6.h... Generating docs for file Rules.h... Generating docs for file SequenceRule.h... Generating docs for file Sort.h... Generating docs for file TooManyNodesException.h... Generating docs for file Conformer.h... Generating docs for file DepictUtils.h... Generating docs for file EmbeddedFrag.h... Generating docs for file RDDepictor.h... Generating docs for file Templates.h... Generating docs for file TemplateSmiles.h... Generating docs for file Deprotect.h... Generating docs for file AtomFeat.h... Generating docs for file AUTOCORR2D.h... Generating docs for file AUTOCORR3D.h... Generating docs for file BCUT.h... Generating docs for file ConnectivityDescriptors.h... Generating docs for file CoulombMat.h... Generating docs for file Crippen.h... Generating docs for file Data3Ddescriptors.h... Generating docs for file DCLV.h... Generating docs for file EEM.h... Generating docs for file GETAWAY.h... Generating docs for file Lipinski.h... Generating docs for file MolData3Ddescriptors.h... Generating docs for file MolDescriptors.h... Generating docs for file MolDescriptors3D.h... Generating docs for file MolSurf.h... Generating docs for file MORSE.h... Generating docs for file MQN.h... Generating docs for file OxidationNumbers.h... Generating docs for file PBF.h... Generating docs for file PMI.h... Generating docs for file Property.h... Generating docs for file RDF.h... Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... Generating docs for file CDXMLParser.h... Generating docs for file FileParsers.h... Generating docs for file FileParserUtils.h... Generating docs for file FileWriters.h... Generating docs for file GeneralFileReader.h... Generating docs for file MaestroProperties.h... Generating docs for file MolFileStereochem.h... Generating docs for file MolSGroupParsing.h... Generating docs for file MolSGroupWriting.h... Generating docs for file MolSupplier.h... Generating docs for file MolSupplier.v1API.h... Generating docs for file MolWriters.h... Generating docs for file MultithreadedMolSupplier.h... Generating docs for file MultithreadedSDMolSupplier.h... Generating docs for file MultithreadedSmilesMolSupplier.h... Generating docs for file PNGParser.h... Generating docs for file ProximityBonds.h... 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Generating docs for file DuplicatedSeedCache.h... Generating docs for file FMCS.h... Generating docs for file Graph.h... Generating docs for file MatchTable.h... Generating docs for file MaximumCommonSubgraph.h... Generating docs for file Seed.h... Generating docs for file SeedSet.h... Generating docs for file SubstructMatchCustom.h... Generating docs for file SubstructureCache.h... Generating docs for file Target.h... Generating docs for file TargetMatch.h... Generating docs for file TorsionAngleContribs.h... Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionPreferences.h... Generating docs for file FFConvenience.h... Generating docs for file MMFF.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file Builder.h... Generating docs for file Builder.h... Generating docs for file UFF.h... Generating docs for file FragCatalogEntry.h... Generating docs for file FragCatalogUtils.h... 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Gener/build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' ating docs for file MolDraw2DSVG.h... Generating docs for file MolDraw2DUtils.h... Generating docs for file MolDraw2Dwx.h... Generating docs for file DrawTextFTQt.h... Generating docs for file DrawTextQt.h... Generating docs for file MolDraw2DQt.h... Generating docs for file StringRect.h... Generating docs for file LinkNode.h... Generating docs for file MolEnumerator.h... Generating docs for file mf.h... Generating docs for file MolHash.h... Generating docs for file nmmolhash.h... Generating docs for file details.h... Generating docs for file details.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... Generating docs for file MolProcessing.h... 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Generating docs for file MolTransforms.h... Generating docs for file MonomerInfo.h... Generating docs for file new_canon.h... Generating docs for file GasteigerCharges.h... Generating docs for file GasteigerParams.h... Generating docs for file PeriodicTable.h... Generating docs for file QueryAtom.h... Generating docs for file QueryBond.h... Generating docs for file QueryOps.h... Generating docs for file PartitionSet.h... Generating docs for file RascalClusterOptions.h... Generating docs for file RascalDetails.h... Generating docs for file RascalMCES.h... Generating docs for file RascalOptions.h... Generating docs for file RascalResult.h... Generating docs for file RDKitBase.h... Generating docs for file RDKitQueries.h... Generating docs for file ReducedGraphs.h... Generating docs for file Resonance.h... Generating docs for file RGroupCore.h... Generating docs for file RGroupData.h... Generating docs for file RGroupDecomp.h... Generating docs for file RGroupDecompData.h... Generating docs for file RGroupDecompParams.h... Generating docs for file RGroupFingerprintScore.h... Generating docs for file RGroupGa.h... Generating docs for file RGroupMatch.h... Generating docs for file RGroupScore.h... Generating docs for file RGroupUtils.h... Generating docs for file RingInfo.h... Generating docs for file Rings.h... Generating docs for file ROMol.h... Generating docs for file RWMol.h... Generating docs for file SanitException.h... Generating docs for file detail.h... Generating docs for file ScaffoldNetwork.h... Generating docs for file ShapeEncoder.h... Generating docs for file ShapeUtils.h... Generating docs for file SLNAttribs.h... Generating docs for file SLNParse.h... Generating docs for file SLNParseOps.h... Generating docs for file CanonicalizeStereoGroups.h... Generating docs for file primes.h... Generating docs for file SmartsWrite.h... Generating docs for file SmilesParse.h... Generating docs for file SmilesParseOps.h... Generating docs for file SmilesWrite.h... Generating docs for file StereoGroup.h... Generating docs for file Pattern.h... Generating docs for file ReCharge.h... Generating docs for file Stereo.h... Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... Generating docs for file SubstanceGroup.h... Generating docs for file SubstructMatch.h... Generating docs for file SubstructUtils.h... Generating docs for file PatternFactory.h... Generating docs for file SubstructLibrary.h... Generating docs for file SubstructLibrarySerialization.h... Generating docs for file TautomerQuery.h... Generating docs for file Snapshot.h... Generating docs for file Trajectory.h... Generating docs for file CorrMatGenerator.h... Generating docs for file InfoBitRanker.h... Generating docs for file InfoGainFuncs.h... Generating docs for file AlignPoints.h... Generating docs for file Conrec.h... Generating docs for file PowerEigenSolver.h... Generating docs for file Matrix.h... Generating docs for file BFGSOpt.h... Generating docs for file SquareMatrix.h... Generating docs for file SymmMatrix.h... Generating docs for file Vector.h... Generating docs for file AndQuery.h... Generating docs for file EqualityQuery.h... Generating docs for file GreaterEqualQuery.h... Generating docs for file GreaterQuery.h... Generating docs for file LessEqualQuery.h... Generating docs for file LessQuery.h... Generating docs for file NullQueryAlgebra.h... Generating docs for file OrQuery.h... Generating docs for file Query.h... Generating docs for file QueryObjects.h... Generating docs for file RangeQuery.h... Generating docs for file SetQuery.h... Generating docs for file XOrQuery.h... Generating docs for file boost_numpy.h... Generating docs for file import_array.h... Generating docs for file pyint_api.h... Generating docs for file PySequenceHolder.h... Generating docs for file python.h... Generating docs for file python_streambuf.h... Generating docs for file BadFileException.h... Generating docs for file BoostEndInclude.h... Generating docs for file BoostStartInclude.h... Generating docs for file ConcurrentQueue.h... Generating docs for file Dict.h... Generating docs for file Exceptions.h... Generating docs for file export.h... Generating docs for file FileParseException.h... Generating docs for file hanoiSort.h... Generating docs for file Invariant.h... Generating docs for file LocaleSwitcher.h... Generating docs for file Ranking.h... Generating docs for file RDAny.h... Generating docs for file RDConfig.h... Generating docs for file RDExportMacros.h... Generating docs for file RDLog.h... Generating docs for file RDProps.h... Generating docs for file RDThreads.h... Generating docs for file RDValue-doublemagic.h... Generating docs for file RDValue-taggedunion.h... Generating docs for file RDValue.h... Generating docs for file StreamOps.h... Generating docs for file types.h... Generating docs for file utils.h... Generating docs for file versions.h... Generating docs for file DistPicker.h... Generating docs for file HierarchicalClusterPicker.h... Generating docs for file LeaderPicker.h... Generating docs for file MaxMinPicker.h... Generating page documentation... Generating docs for page deprecated... Generating group documentation... Generating class documentation... Generating docs for compound BitVect... Generating docs for compound Data3Ddescriptors... Generating docs for compound DatastructsException... Generating docs for compound ExplicitBitVect... Generating docs for compound IndexErrorException... Generating docs for compound KeyErrorException... Generating docs for compound MolData3Ddescriptors... Generating docs for compound PySequenceHolder... Generating docs for compound SparseBitVect... Generating docs for compound ValueErrorException... Generating concept documentation... Generating module documentation... Generating namespace documentation... Generating docs for namespace BFGSOpt Generating docs for namespace boost Generating docs for namespace boost::logging Generating docs for compound boost::logging::rdLogger... Generating docs for namespace boost_adaptbx Generating docs for namespace boost_adaptbx::python Generating docs for compound boost_adaptbx::python::ostream... Generating docs for compound boost_adaptbx::python::streambuf... Generating docs for nested compound boost_a/build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistGeomUtils.h:93: warning: The following parameter of DistGeom::constructForceField(const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets, double weightChiral=1.0, double weightFourthDim=0.1, std::map< std::pair< int, int >, double > *extraWeights=nullptr, double basinSizeTol=5.0, boost::dynamic_bitset<> *fixedPts=nullptr) is not documented: parameter 'fixedPts' /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContribs.h:46: warning: argument 'cset' of command @param is not found in the argument list of DistGeom::ChiralViolationContribs::ChiralViolationContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContribs.h:46: warning: argument 'weight' of command @param is not found in the argument list of DistGeom::ChiralViolationContribs::ChiralViolationContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202409.2/Code/DistGeom/FourthDimContribs.h:36: warning: argument 'idx' of command @param is not found in the argument list of DistGeom::FourthDimContribs::FourthDimContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202409.2/Code/DistGeom/FourthDimContribs.h:36: warning: argument 'weight' of command @param is not found in the argument list of DistGeom::FourthDimContribs::FourthDimContribs(ForceFields::ForceField *owner) /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraint.h:24: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraint.h:24: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraint.h:24: warning: The following parameters of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.h:65: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.h:65: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.h:65: warning: The following parameters of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.h:53: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.h:53: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.h:53: warning: The following parameters of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.h:61: warning: argument 'forceConst' of command @param is not found in the argument list of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, bool relative, double minLen, double maxLen, double forceConstant) /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.h:61: warning: The following parameter of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, bool relative, double minLen, double maxLen, double forceConstant) is not documented: parameter 'forceConstant' /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.h:50: warning: argument 'forceConst' of command @param is not found in the argument list of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, double minLen, double maxLen, double forceConstant) /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.h:50: warning: The following parameter of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, double minLen, double maxLen, double forceConstant) is not documented: parameter 'forceConstant' /build/reproducible-path/rdkit-202409.2/Code/ForceField/ForceField.h:159: warning: argument 'snapshotFreq' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/reproducible-path/rdkit-202409.2/Code/ForceField/ForceField.h:159: warning: argument 'snapshotVect' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/reproducible-path/rdkit-202409.2/Code/ForceField/ForceField.h:144: warning: The following parameters of ForceFields::ForceField::minimize(unsigned int snapshotFreq, RDKit::SnapshotVect *snapshotVect, unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) are not documented: parameter 'snapshotFreq' parameter 'snapshotVect' /build/reproducible-path/rdkit-202409.2/Code/ForceField/PositionConstraint.h:25: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/AngleBend.h:31: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/AngleBend.h:31: warning: The following parameters of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) are not documented: parameter 'mmffAngleParams' parameter 'mmffPropParamsCentralAtom' /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'bondType' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end1Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end2Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/BondStretch.h:28: warning: The following parameter of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) is not documented: parameter 'mmffBondParams' /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Nonbonded.h:54: warning: The following parameters of ForceFields::MMFF::EleContrib::EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, double chargeTerm, std::uint8_t dielModel, bool is1_4) are not documented: parameter 'chargeTerm' parameter 'dielModel' parameter 'is1_4' daptbx::python::streambuf::istream... Generating docs for nested compound boost_adaptbx::python::streambuf::ostream... Generating docs for compound boost_adaptbx::python::streambuf_capsule... Generating docs for namespace ChemicalFeatures Generating docs for compound ChemicalFeatures::ChemicalFeature... Generating docs for compound ChemicalFeatures::FreeChemicalFeature... Generating docs for namespace conrec Generating docs for compound conrec::ConrecSegment... Generating docs for compound conrec::tplHash... Generating docs for namespace DistGeom Generating docs for compound DistGeom::BoundsMatrix... Generating docs for compound DistGeom::ChiralSet... Generating docs for compound DistGeom::ChiralViolationContrib... Generating docs for compound DistGeom::ChiralViolationContribs... Generating docs for compound DistGeom::ChiralViolationContribsParams... Generating docs for compound DistGeom::DistViolationContrib... Generating docs for compound DistGeom::DistViolationContribs... Generating docs for compound DistGeom::DistViolationContribsParams... Generating docs for compound DistGeom::FourthDimContrib... Generating docs for compound DistGeom::FourthDimContribs... Generating docs for compound DistGeom::FourthDimContribsParams... Generating docs for namespace ForceFields Generating docs for compound ForceFields::AngleConstraintContrib... Generating docs for compound ForceFields::AngleConstraintContribs... Generating docs for compound ForceFields::AngleConstraintContribsParams... Generating docs for compound ForceFields::DistanceConstraintContrib... Generating docs for compound ForceFields::DistanceConstraintContribs... Generating docs for compound ForceFields::DistanceConstraintContribsParams... Generating docs for compound ForceFields::ForceField... Generating docs for compound ForceFields::ForceFieldContrib... Generating docs for compound ForceFields::PositionConstraintContrib... Generating docs for compound ForceFields::TorsionConstraintContrib... Generating docs for namespace ForceFields::CrystalFF Generating docs for compound ForceFields::CrystalFF::CrystalFFDetails... Generating docs for compound ForceFields::CrystalFF::ExpTorsionAngle... Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribM6... Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribs... Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribsParams... Generating docs for namespace ForceFields::MMFF Generating docs for compound ForceFields::MMFF::AngleBendContrib... Generating docs for compound ForceFields::MMFF::BondStretchContrib... Generating docs for compound ForceFields::MMFF::EleContrib... Generating docs for compound ForceFields::MMFF::MMFFAngle... Generating docs for compound ForceFields::MMFF::MMFFAngleCollection... Generating docs for compound ForceFields::MMFF::MMFFAromCollection... Generating docs for compound ForceFields::MMFF::MMFFBndkCollection... Generating docs for compound ForceFields::MMFF::MMFFBond... Generating docs for compound ForceFields::MMFF::MMFFBondCollection... Generating docs for compound ForceFields::MMFF::MMFFChg... Generating docs for compound ForceFields::MMFF::MMFFChgCollection... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEle... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEleCollection... Generating docs for compound ForceFields::MMFF::MMFFDef... Generating docs for compound ForceFields::MMFF::MMFFDefCollection... Generating docs for compound ForceFields::MMFF::MMFFDfsbCollection... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurie... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurieCollection... Generating docs for compound ForceFields::MMFF::MMFFOop... Generating docs for compound ForceFields::MMFF::MMFFOopCollection... Generating docs for compound ForceFields::MMFF::MMFFPBCI... Generating docs for compound ForceFields::MMFF::MMFFPBCICollection... Generating docs for compound ForceFields::MMFF::MMFFProp... Generating docs for compound ForceFields::MMFF::MMFFPropCollection... Generating docs /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/StretchBend.h:32: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/StretchBend.h:32: warning: The following parameters of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) are not documented: parameter 'mmffStbnParams' parameter 'mmffAngleParams' parameter 'mmffBondParams1' parameter 'mmffBondParams2' /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/TorsionAngle.h:31: warning: argument 'torsionType' of command @param is not found in the argument list of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/TorsionAngle.h:31: warning: The following parameter of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) is not documented: parameter 'mmffTorParams' /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Nonbonded.h:30: warning: The following parameter of ForceFields::MMFF::VdWContrib::VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants) is not documented: parameter 'mmffVdWConstants' /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Inversion.h:27: warning: The following parameter of ForceFields::UFF::InversionContrib::InversionContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, int at2AtomicNum, bool isCBoundToO, double oobForceScalingFactor=1.0) is not documented: parameter 'oobForceScalingFactor' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/RDDepictor.h:393: warning: argument 'refPattern' of command @param is not found in the argument list of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/RDDepictor.h:393: warning: The following parameter of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) is not documented: parameter 'referencePattern' for compound ForceFields::MMFF::MMFFStbn... Generating docs for compound ForceFields::MMFF::MMFFStbnCollection... Generating docs for compound ForceFields::MMFF::MMFFTor... Generating docs for compound ForceFields::MMFF::MMFFTorCollection... Generating docs for compound ForceFields::MMFF::MMFFVdW... Generating docs for compound ForceFields::MMFF::MMFFVdWCollection... Generating docs for compound ForceFields::MMFF::MMFFVdWRijstarEps... Generating docs for compound ForceFields::MMFF::OopBendContrib... Generating docs for compound ForceFields::MMFF::StretchBendContrib... Generating docs for compound ForceFields::MMFF::TorsionAngleContrib... Generating docs for compound ForceFields::MMFF::VdWContrib... Generating docs for namespace ForceFields::MMFF::Utils Generating docs for namespace ForceFields::UFF Generating docs for compound ForceFields::UFF::AngleBendContrib... Generating docs for compound ForceFields::UFF::AtomicParams... Generating docs for compound ForceFields::UFF::BondStretchContrib... Generating docs for compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::InversionContribs... Generating docs for compound ForceFields::UFF::InversionContribsParams... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for namespace ForceFields::UFF::Params Generating docs for namespace ForceFields::UFF::Utils Generating docs for namespace Invar Generating docs for compound Invar::Invariant... Generating docs for namespace MolTransforms Generating docs for namespace Queries Generating docs for compound Queries::AndQuery... Generating docs for compound Queries::EqualityQuery... Generating docs for compound Queries::GreaterEqualQuery... Generating docs for compound Queries::GreaterQuery... Generating docs for compound Queries::Int2Type... Generating docs for compound Queries::LessEqualQuery... Generating docs for compound Queries::LessQuery... Generating docs for compound Queries::OrQuery... Generating docs for compound Queries::Query... Generating docs for compound Queries::RangeQuery... Generating docs for compound Queries::SetQuery... Generating docs for compound Queries::XOrQuery... Generating docs for namespace Rankers Generating docs for namespace RDCatalog Generating docs for compound RDCatalog::Catalog... Generating docs for compound RDCatalog::CatalogEntry... Generating docs for compound RDCatalog::CatalogParams... Generating docs for compound RDCatalog::HierarchCatalog... Generating docs for nested compound RDCatalog::HierarchCatalog::vertex_entry_t... Generating docs for namespace RDDataManip Generating docs for compound RDDataManip::MetricMatrixCalc... Generating docs for namespace RDDepict Generating docs for compound RDDepict::Compute2DCoordParameters... Generating docs for compound RDDepict::ConstrainedDepictionParams... Generating docs for compound RDDepict::CoordinateTemplates... Generating docs for compound RDDepict::DepictException... Generating docs for compound RDDepict::EmbeddedAtom... Generating docs for compound RDDepict::EmbeddedFrag... Generating docs for compound RDDepict::gtIIPair... Generating docs for namespace RDFeatures Generating docs for compound RDFeatures::ExplicitFeature... Generating docs for compound RDFeatures::ImplicitFeature... Generating docs for namespace RDGeom Generating docs for compound RDGeom::Grid3D... Generating docs for compound RDGeom::GridException... Generating docs for compound RDGeom::Point... Generating docs for compound RDGeom::Point2D... Generating docs for compound RDGeom::Point3D... Generating docs for compound RDGeom::PointND... Generating docs for compound RDGeom::Transform2D... Generating/build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstanceGroup.h:276: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: argument 'seq' of command @param is not found in the argument list of RDKit::HELMToMol(const char *helm, bool sanitize=true) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: The following parameter of RDKit::HELMToMol(const char *helm, bool sanitize=true) is not documented: parameter 'helm' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Fingerprints.h:69: warning: The following parameter of RDKit::LayeredFingerprintMol(const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool branchedPaths=true, const std::vector< std::uint32_t > *fromAtoms=nullptr) is not documented: parameter 'fromAtoms' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesWrite.h:229: warning: argument 'doRandom' of command @param is not found in the argument list of RDKit::MolFragmentToSmiles(const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:35: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:35: warning: The following parameter of RDKit::MolToMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:110: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:110: warning: The following parameter of RDKit::MolToMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinParser.h:180: warning: The following parameters of RDKit::MolToMrvBlock(const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) are not documented: parameter 'mol' parameter 'includeStereo' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinParser.h:155: warning: The following parameters of RDKit::MolToMrvFile(const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) are not documented: parameter 'mol' parameter 'fName' parameter 'includeStereo' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:226: warning: argument 'fName' of command @param is not found in the argument list of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:226: warning: The following parameter of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) is not documented: parameter 'fname' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:96: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV2KMolBlock(const ROMol &mol, const MolWriterParams ¶ms=MolWriterParams(), int confId=-1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:96: warning: The following parameter of RDKit::MolToV2KMolBlock(const ROMol &mol, const MolWriterParams ¶ms=MolWriterParams(), int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:65: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV3KMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:65: warning: The following parameter of RDKit::MolToV3KMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:141: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV3KMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileWriters.h:141: warning: The following parameter of RDKit::MolToV3KMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Fingerprints.h:120: warning: The following parameter of RDKit::PatternFingerprintMol(const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false) is not documented: parameter 'tautomericFingerprint' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: argument 'useBondOrders' of command @param is not found in the argument list of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: The following parameters of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) are not documented: parameter 'useBondOrder' parameter 'bitInfo' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionRunner.h:94: warning: The following parameter of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) is not documented: parameter 'product' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/ChemTransforms.h:114: warning: argument 'useChirality' of command @param is not found in the argument list of RDKit::replaceCore(const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: argument 'reactantTemplateIdx' of command @param is not found in the argument list of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: The following parameters of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) are not documented: parameter 'rxn' parameter 'reactantIdx' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructMatch.h:81: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructMatch.h:81: warning: The following parameter of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructMatch.h:94: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructMatch.h:94: warning: The following parameter of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructMatch.h:149: warning: The following parameter of RDKit::SubstructMatch(T1 &mol, const T2 &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000, int numThreads=1) is not documented: parameter 'numThreads' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::AtomEnvironment::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const=0 are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Reaction.h:219: warning: argument 'maxProducts' of command @param is not found in the argument list of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Reaction.h:219: warning: The following parameter of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const is not documented: parameter 'numProducts' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatchers.h:430: warning: argument 'matches' of command @param is not found in the argument list of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 is not documented: parameter 'matchVect' docs for compound RDGeom::Transform3D... Generating docs for compound RDGeom::UniformGrid3D... Generating docs for namespace RDInfoTheory Generating docs for compound RDInfoTheory::BitCorrMatGenerator... Generating docs for compound RDInfoTheory::InfoBitRanker... Generating docs for namespace RDKit Generating docs for compound RDKit::AdditionalOutput... Generating docs for compound RDKit::AromaticAtomIterator_... Generating docs for compound RDKit::Atom... Generating docs for compound RDKit::AtomEnvironment... Generating docs for compound RDKit::AtomEnvironmentGenerator... Generating docs for compound RDKit::atomicData... Generating docs for compound RDKit::AtomInvariantsGenerator... Generating docs for compound RDKit::AtomIterator_... Generating docs for compound RDKit::AtomKekulizeException... Generating docs for compound RDKit::AtomMonomerInfo... Generating docs for compound RDKit::AtomPDBResidueInfo... Generating docs for compound RDKit::AtomRingQuery... Generating docs for compound RDKit::AtomSanitizeException... Generating docs for compound RDKit::AtomValenceException... Generating docs for compound RDKit::BadFileException... Generating docs for compound RDKit::Bond... Generating docs for compound RDKit::BondInvariantsGenerator... Generating docs for compound RDKit::BondIterator_... Generating docs for compound RDKit::CachedMolHolder... Generating docs for compound RDKit::CachedSmilesMolHolder... Generating docs for compound RDKit::CachedTrustedSmilesMolHolder... Generating docs for compound RDKit::CartesianProduct... Generating docs for compound RDKit::CartesianProductStrategy... Generating docs for compound RDKit::charptr_functor... Generating docs for compound RDKit::ChemicalReaction... Generating docs for compound RDKit::ChemicalReactionException... Generating docs for compound RDKit::ChemicalReactionParserException... Generating docs for compound RDKit::Conformer... Generating docs for compound RDKit::ConformerException... Generating docs for compound RDKit::ConstBondIterator_... Generating docs for compound RDKit::CustomPropHandler... Generating docs for compound RDKit::CXXAtomIterator... Generating docs for nested compound RDKit::CXXAtomIterator::CXXAtomIter... Generating docs for compound RDKit::CXXBondIterator... Generating docs for nested compound RDKit::CXXBondIterator::CXXBondIter... Generating docs for compound RDKit::DataStructsExplicitBitVecPropHandler... Generating docs for compound RDKit::Dict... Generating docs for nested compound RDKit::Dict::Pair... Generating docs for compound RDKit::DiscreteDistMat... Generating docs for compound RDKit::DiscreteValueVect... Generating docs for compound RDKit::DrawColour... Generating docs for compound RDKit::EnumerateLibrary... Generating docs for compound RDKit::EnumerateLibraryBase... Generating docs for compound RDKit::EnumerationParams... Generating docs for compound RDKit::EnumerationStrategyBase... Generating docs for compound RDKit::EnumerationStrategyException... Generating docs for compound RDKit::EvenSamplePairsStrategy... Generating docs for compound RDKit::ExclusionList... Generating docs for compound RDKit::FeatureFileParseException... Generating docs for compound RDKit::FileParseException... Generating docs for compound RDKit::FilterCatalog... Generating docs for compound RDKit::FilterCatalogEntry... Generating docs for compound RDKit::FilterCatalogParams... Generating docs for compound RDKit::FilterData_t... Generating docs for compound RDKit::FilterHierarchyMatcher... Generating docs for compound RDKit::FilterMatch... Generating docs for compound RDKit::FilterMatcherBase... Generating docs for compound RDKit::FilterProperty_t... Generating docs for compound RDKit::FingerprintArguments... Generating docs for compound RDKit::FingerprintFuncArguments... Generating docs for compound RDKit::FingerprintGenerator... Generating docs for compound RDKit::FingerprintVarianceScoreData... Generating docs for compound RDKit::FixedMolSizeMolBundle... Generating docs for compound RDKit::FPBReader... Generating docs for compound RDKit::FPHolderBase... Generati/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecule has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: The following parameter of RDKit::MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1) is not documented: parameter 'highlight_bonds' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_atom_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_bond_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'confId' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecules has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: The following parameters of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) are not documented: parameter 'highlight_bonds' parameter 'highlight_atom_maps' parameter 'highlight_bond_maps' parameter 'confIds' ng docs for compound RDKit::FragCatalogEntry... Generating docs for compound RDKit::FragCatGenerator... Generating docs for compound RDKit::FragCatParams... Generating docs for compound RDKit::FragFPGenerator... Generating docs for compound RDKit::GaResult... Generating docs for compound RDKit::GasteigerParams... Generating docs for compound RDKit::HasPropQuery... Generating docs for compound RDKit::HasPropWithValueQuery... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, std::string >... Generating docs for compound RDKit::HasPropWithValueQueryBase... Generating docs for compound RDKit::HeteroatomIterator_... Generating docs for compound RDKit::KekulizeException... Generating docs for compound RDKit::KeyFromPropHolder... Generating docs for compound RDKit::KeyHolderBase... Generating docs for compound RDKit::larger_of... Generating docs for compound RDKit::ltDouble... Generating docs for compound RDKit::MarvinArrow... Generating docs for compound RDKit::MarvinAtom... Generating docs for compound RDKit::MarvinAttachmentPoint... Generating docs for compound RDKit::MarvinBond... Generating docs for compound RDKit::MarvinBondStereo... Generating docs for compound RDKit::MarvinCondition... Generating docs for compound RDKit::MarvinDataSgroup... Generating docs for compound RDKit::MarvinGenericSgroup... Generating docs for compound RDKit::MarvinMol... Generating docs for compound RDKit::MarvinMolBase... Generating docs for compound RDKit::MarvinMonomerSgroup... Generating docs for compound RDKit::MarvinMulticenterSgroup... Generating docs for compound RDKit::MarvinMultipleSgroup... Generating docs for compound RDKit::MarvinPlus... Generating docs for compound RDKit::MarvinReaction... Generating docs for compound RDKit::MarvinRectangle... Generating docs for compound RDKit::MarvinSruCoModSgroup... Generating docs for compound RDKit::MarvinStereoGroup... Generating docs for compound RDKit::MarvinSuperatomSgroup... Generating docs for compound RDKit::MarvinSuperatomSgroupExpanded... Generating docs for compound RDKit::MarvinWriterException... Generating docs for compound RDKit::MatchingAtomIterator_... Generating docs for compound RDKit::MCSAtomCompareParameters... Generating docs for compound RDKit::MCSBondCompareParameters... Generating docs for compound RDKit::MCSParameters... Generating docs for compound RDKit::MCSProgressData... Generating docs for compound RDKit::MCSResult... Generating docs for compound RDKit::MolBundle... Generating docs for compound RDKit::MolCatalogEntry... Generating docs for compound RDKit::MolCatalogParams... Generating docs for compound RDKit::MolChemicalFeature... Generating docs for compound RDKit::MolChemicalFeatureDef... Generating docs for compound RDKit::MolChemicalFeatureFactory... Generating docs for compound RDKit::MolDraw2D... Generating docs for compound RDKit::MolDraw2DCairo... Generating docs for compound RDKit::MolDraw2DJS... Generating docs for compound RDKit::MolDraw2DQt... Generating docs for compound RDKit::MolDraw2DSVG... Generating docs for compound RDKit::MolDraw2Dwx... Generating docs for compound RDKit::MolDrawOptions... Generating docs for compound RDKit::MolHolder... Generating docs for compound RDKit::MolHolderBase... Generating docs for compound RDKit::MolMatchFinalCheckFunctor... Generating docs for compound RDKit::MolPickler... Generating docs for compound RDKit::MolPicklerException... Generating docs for compound RDKit::MolSanitizeException... Generating docs for compound RDKit::MolWriter... Generating docs for compound RDKit::MolWriterParams... Generating docs for compound RDKit::MolzipParams... Generating docs for compound RDKit::MrvWriterParams... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::PatternHolder... Generating docs for compound RDKit::PDBWriter... Generating docs for compound RDKit::PeriodicTable... Generating docs for compound RDKit::QueryAtom... Generating docs for compound RDKit::QueryAtomIterator_../build/reproducible-path/rdkit-202409.2/Code/GraphMol/Resonance.h:114: warning: argument 'numThreads' of command @param is not found in the argument list of RDKit::ResonanceMolSupplier::ResonanceMolSupplier(ROMol &mol, unsigned int flags=0, unsigned int maxStructs=1000) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatchers.h:336: warning: argument 'matches' of command @param is not found in the argument list of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/Abbreviations.h:104: warning: The following parameter of RDKit::Abbreviations::findApplicableAbbreviationMatches(const ROMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::AtomPair::AtomPairAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/AtomPairs.h:97: warning: The following parameter of RDKit::AtomPairs::getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false, bool use2D=true, int confId=-1) is not documented: parameter 'confId' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintUtil.h:75: warning: The following parameter of RDKit::AtomPairs::getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false) is not documented: parameter 'includeChirality' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Canon.h:98: warning: The following parameters of RDKit::Canon::canonicalizeFragment(ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, const std::vector< unsigned int > &ranks, MolStack &molStack, const boost::dynamic_bitset<> *bondsInPlay=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=false, bool doRandom=false, bool doChiralInversions=true) are not documented: parameter 'bondsInPlay' parameter 'bondSymbols' parameter 'doIsomericSmiles' parameter 'doRandom' parameter 'doChiralInversions' . Generating docs for compound RDKit::QueryBond... Generating docs for compound RDKit::RandomSampleAllBBsStrategy... Generating docs for compound RDKit::RandomSampleStrategy... Generating docs for compound RDKit::RCore... Generating docs for compound RDKit::RDAny... Generating docs for compound RDKit::RDProps... Generating docs for compound RDKit::RDValue... Generating docs for compound RDKit::ReactionFingerprintParams... Generating docs for compound RDKit::ReactionPickler... Generating docs for compound RDKit::ReactionPicklerException... Generating docs for compound RDKit::RecursiveStructureQuery... Generating docs for compound RDKit::ResonanceMolSupplier... Generating docs for compound RDKit::ResonanceMolSupplierCallback... Generating docs for compound RDKit::RGroupData... Generating docs for compound RDKit::RGroupDecompData... Generating docs for nested compound RDKit::RGroupDecompData::UsedLabels... Generating docs for compound RDKit::RGroupDecomposition... Generating docs for compound RDKit::RGroupDecompositionChromosome... Generating docs for compound RDKit::RGroupDecompositionParameters... Generating docs for compound RDKit::RGroupDecompositionProcessResult... Generating docs for compound RDKit::RGroupGa... Generating docs for compound RDKit::RGroupMatch... Generating docs for compound RDKit::RGroupScorer... Generating docs for compound RDKit::RigorousEnhancedStereoException... Generating docs for compound RDKit::RingInfo... Generating docs for compound RDKit::ROMol... Generating docs for compound RDKit::RWMol... Generating docs for compound RDKit::RxnSanitizeException... Generating docs for compound RDKit::SDWriter... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::SmilesWriteParams... Generating docs for compound RDKit::SmilesWriter... Generating docs for compound RDKit::Snapshot... Generating docs for compound RDKit::SparseIntVect... Generating docs for compound RDKit::StereoBondThresholds... Generating docs for compound RDKit::StereoGroup... Generating docs for compound RDKit::SubstanceGroup... Generating docs for nested compound RDKit::SubstanceGroup::AttachPoint... Generating docs for nested compound RDKit::SubstanceGroup::CState... Generating docs for compound RDKit::SubstanceGroupException... Generating docs for compound RDKit::SubstructLibrary... Generating docs for compound RDKit::SubstructMatchParameters... Generating docs for compound RDKit::TautomerPatternHolder... Generating docs for compound RDKit::TautomerQuery... Generating docs for compound RDKit::TDTWriter... Generating docs for compound RDKit::Trajectory... Generating docs for compound RDKit::UnimplementedFPException... Generating docs for compound RDKit::UsedLabelMap... Generating docs for compound RDKit::VarianceDataForLabel... Generating docs for namespace RDKit::Abbreviations Generating docs for compound RDKit::Abbreviations::AbbreviationDefinition... Generating docs for compound RDKit::Abbreviations::AbbreviationMatch... Generating docs for namespace RDKit::Abbreviations::common_properties Generating docs for namespace RDKit::Abbreviations::Utils Generating docs for namespace RDKit::AtomPair Generating docs for compound RDKit::AtomPair::AtomPairArguments... Generating docs for compound RDKit::AtomPair::AtomPairAtomEnv... Generating docs for compound RDKit::AtomPair::AtomPairAtomInvGenerator... Generating docs for compound RDKit::AtomPair::AtomPairEnvGenerator... Generating docs for namespace RDKit::AtomPairs Generating docs for namespace RDKit::Atropisomers Generating docs for namespace RDKit::Canon Generating docs for compound RDKit::Canon::AtomCompareFunctor... Generating docs for compound RDKit::Canon::bondholder... Generating docs for compound RDKit::Canon::canon_atom... Generating docs for compound RDKit::Canon::ChiralAtomCompareFunctor... Generating docs for compound RDKit::Canon::MolStackElem... Generating docs for compound RDKit::Canon::MolStackUnion... Generating docs for compound RDKit::Canon::SpecialChiralityAtomCompareFunctor... Ge/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Chirality.h:404: warning: The following parameters of RDKit::Chirality::findMesoCenters(const ROMol &mol, bool includeIsotopes=true, bool includeAtomMaps=false) are not documented: parameter 'includeIsotopes' parameter 'includeAtomMaps' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Chirality.h:142: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented: parameter 'flagPossible' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Chirality.h:194: warning: The following parameter of RDKit::Chirality::getTrigonalBipyramidalAxialBond(const Atom *center, int which=0) is not documented: parameter 'center' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPLabeler.h:44: warning: The following parameter of RDKit::CIPLabeler::assignCIPLabels(ROMol &mol, unsigned int maxRecursiveIterations=0) is not documented: parameter 'maxRecursiveIterations' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Lipinski.h:45: warning: argument 'strict' of command @param is not found in the argument list of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Lipinski.h:45: warning: The following parameter of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) is not documented: parameter 'useStrictDefinition' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/USRDescriptor.h:68: warning: The following parameter of RDKit::Descriptors::USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int > > &atomIds, int confId=-1) is not documented: parameter 'atomIds' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:37: warning: The following parameter of RDKit::DGeomHelpers::setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds=true, bool scaleVDW=false, bool useMacrocycle14config=false, bool forceTransAmides=true) is not documented: parameter 'forceTransAmides' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatchers.h:98: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatchers.h:218: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatchers.h:161: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' nerating docs for compound RDKit::Canon::SpecialSymmetryAtomCompareFunctor... Generating docs for namespace RDKit::Canon::detail Generating docs for namespace RDKit::Chirality Generating docs for compound RDKit::Chirality::BondWedgingParameters... Generating docs for compound RDKit::Chirality::StereoInfo... Generating docs for compound RDKit::Chirality::WedgeInfoAtropisomer... Generating docs for compound RDKit::Chirality::WedgeInfoBase... Generating docs for compound RDKit::Chirality::WedgeInfoChiral... Generating docs for namespace RDKit::Chirality::detail Generating docs for namespace RDKit::CIPLabeler Generating docs for compound RDKit::CIPLabeler::AtropisomerBond... Generating docs for compound RDKit::CIPLabeler::CIPMol... Generating docs for compound RDKit::CIPLabeler::CIPMolSpan... Generating docs for nested compound RDKit::CIPLabeler::CIPMolSpan::CIPMolIter... Generating docs for compound RDKit::CIPLabeler::Configuration... Generating docs for compound RDKit::CIPLabeler::Digraph... Generating docs for compound RDKit::CIPLabeler::Edge... Generating docs for compound RDKit::CIPLabeler::MaxIterationsExceeded... Generating docs for compound RDKit::CIPLabeler::Node... Generating docs for compound RDKit::CIPLabeler::PairList... Generating docs for compound RDKit::CIPLabeler::Priority... Generating docs for compound RDKit::CIPLabeler::Rule1a... Generating docs for compound RDKit::CIPLabeler::Rule1b... Generating docs for compound RDKit::CIPLabeler::Rule2... Generating docs for compound RDKit::CIPLabeler::Rule3... Generating docs for compound RDKit::CIPLabeler::Rule4a... Generating docs for compound RDKit::CIPLabeler::Rule4b... Generating docs for compound RDKit::CIPLabeler::Rule4c... Generating docs for compound RDKit::CIPLabeler::Rule5... Generating docs for compound RDKit::CIPLabeler::Rule5New... Generating docs for compound RDKit::CIPLabeler::Rule6... Generating docs for compound RDKit::CIPLabeler::Rules... Generating docs for compound RDKit::CIPLabeler::SequenceRule... Generating docs for compound RDKit::CIPLabeler::Sort... Generating docs for compound RDKit::CIPLabeler::Sp2Bond... Generating docs for compound RDKit::CIPLabeler::Tetrahedral... Generating docs for compound RDKit::CIPLabeler::TooManyNodesException... Generating docs for namespace RDKit::CIPLabeler_detail Generating docs for namespace RDKit::common_properties Generating docs for namespace RDKit::constants Generating docs for namespace RDKit::Deprotect Generating docs for compound RDKit::Deprotect::DeprotectData... Generating docs for namespace RDKit::Descriptors Generating docs for compound RDKit::Descriptors::CrippenParamCollection... Generating docs for compound RDKit::Descriptors::CrippenParams... Generating docs for compound RDKit::Descriptors::DoubleCubicLatticeVolume... Generating docs for compound RDKit::Descriptors::Properties... Generating docs for compound RDKit::Descriptors::PropertyFunctor... Generating docs for namespace RDKit::Descriptors::detail Generating docs for namespace RDKit::detail Generating docs for compound RDKit::detail::MCSParametersInternal... Generating docs for namespace RDKit::details Generating docs for namespace RDKit::DGeomHelpers Generating docs for compound RDKit::DGeomHelpers::EmbedParameters... Generating docs for namespace RDKit::DTags Generating docs for namespace RDKit::EnumerationStrategyPickler Generating docs for namespace RDKit::EnumerationTypes Generating docs for namespace RDKit::FileParsers Generating docs for namespace RDKit::FileParsers::schrodinger Generating docs for namespace RDKit::FileParserUtils Generating docs for namespace RDKit::FilterMatchOps Generating docs for compound RDKit::FilterMatchOps::And... Generating docs for compound RDKit::FilterMatchOps::Not... Generating docs for compound RDKit::FilterMatchOps::Or... Generating docs for namespace RDKit::FMCS Generating docs for compound RDKit::FMCS::Composition2N... Generating docs for compound RDKit::FMCS::DuplicatedSeedCache... Generating docs for nested compound RDKit::FMCS::DuplicatedSeedCache::TKey... Generating docs for compound RDKit::FMC/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MHFP.h:93: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::CreateShingling(const ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MHFP.h:132: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::Encode(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MHFP.h:183: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::EncodeSECFP(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1, size_t length=2048) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA.h:23: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int maxCuts=3, unsigned int maxCutBonds=20, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA.h:44: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/AlignMolecules.h:149: warning: argument 'trans' of command @param is not found in the argument list of RDKit::MolAlign::getBestRMS(ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr, int numThreads=1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/AtomSymbol.h:38: warning: The following parameters of RDKit::MolDraw2D_detail::AtomSymbol::AtomSymbol(const std::string &symbol, int atIdx, OrientType orient, const Point2D &cds, const DrawColour &colour, DrawText &textDrawer) are not documented: parameter 'atIdx' parameter 'cds' parameter 'colour' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: The following parameters of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) are not documented: parameter 'bondColours' parameter 'highlight_radii' parameter 'includeAnnotations' parameter 'isReactionMol' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h:24: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h:24: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:36: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCHLasso::DrawMolMCHLasso(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:36: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCHLasso::DrawMolMCHLasso(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' S::ExecStatistics... Generating docs for compound RDKit::FMCS::Graph... Generating docs for compound RDKit::FMCS::MaximumCommonSubgraph... Generating docs for compound RDKit::FMCS::MolFragment... Generating docs for compound RDKit::FMCS::NewBond... Generating docs for compound RDKit::FMCS::Seed... Generating docs for compound RDKit::FMCS::SeedSet... Generating docs for compound RDKit::FMCS::SubstructureCache... Generating docs for nested compound RDKit::FMCS::SubstructureCache::HashKey... Generating docs for nested compound RDKit::FMCS::SubstructureCache::KeyNumericMetrics... Generating docs for compound RDKit::FMCS::Target... Generating docs for compound RDKit::FMCS::TargetMatch... Generating docs for compound RDKit::FMCS::TArray2D... Generating docs for namespace RDKit::ForceFieldsHelper Generating docs for namespace RDKit::ForceFieldsHelper::detail Generating docs for namespace RDKit::GeneralizedSubstruct Generating docs for compound RDKit::GeneralizedSubstruct::ExtendedQueryMol... Generating docs for namespace RDKit::GeneralMolSupplier Generating docs for compound RDKit::GeneralMolSupplier::SupplierOptions... Generating docs for namespace RDKit::GenericGroups Generating docs for namespace RDKit::GenericGroups::Matchers Generating docs for namespace RDKit::Local Generating docs for namespace RDKit::MACCSFingerprints Generating docs for namespace RDKit::MHFPFingerprints Generating docs for compound RDKit::MHFPFingerprints::MHFPEncoder... Generating docs for namespace RDKit::MHFPFingerprints::FNV Generating docs for namespace RDKit::MMFF Generating docs for compound RDKit::MMFF::MMFFAtomProperties... Generating docs for compound RDKit::MMFF::MMFFMolProperties... Generating docs for namespace RDKit::MMFF::DefaultParameters Generating docs for namespace RDKit::MMFF::Tools Generating docs for compound RDKit::MMFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::MMPA Generating docs for namespace RDKit::MolAlign Generating docs for compound RDKit::MolAlign::LAP... Generating docs for compound RDKit::MolAlign::MolAlignException... Generating docs for compound RDKit::MolAlign::MolHistogram... Generating docs for compound RDKit::MolAlign::O3A... Generating docs for compound RDKit::MolAlign::O3AConstraint... Generating docs for compound RDKit::MolAlign::O3AConstraintVect... Generating docs for compound RDKit::MolAlign::O3AFuncData... Generating docs for compound RDKit::MolAlign::SDM... Generating docs for namespace RDKit::MolAlign::details Generating docs for namespace RDKit::MolDraw2D_detail Generating docs for compound RDKit::MolDraw2D_detail::AtomSymbol... Generating docs for compound RDKit::MolDraw2D_detail::DrawAnnotation... Generating docs for compound RDKit::MolDraw2D_detail::DrawMol... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCH... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCHLasso... Generating docs for compound RDKit::MolDraw2D_detail::DrawShape... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArc... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArrow... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeDashedWedge... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeEllipse... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapePolyLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSimpleLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSolidWedge... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeWavyLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawText... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextCairo... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFT... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTCairo... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTJS... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTQt... Generating docs for compound RD/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:263: warning: The following parameter of RDKit::MolEnumerator::enumerate(const ROMol &mol, size_t maxPerOperation=0) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/MolInterchange.h:81: warning: The following parameter of RDKit::MolInterchange::MolsToJSONData(const std::vector< T > &mols, const JSONWriteParameters ¶ms=defaultJSONWriteParameters) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/MolInterchange.h:90: warning: The following parameter of RDKit::MolInterchange::MolToJSONData(const T &mol, const JSONWriteParameters ¶ms=defaultJSONWriteParameters) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolOps.h:330: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) are not documented: parameter 'mergeUnmappedOnly' parameter 'mergeIsotopes' Kit::MolDraw2D_detail::DrawTextFTSVG... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextJS... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextNotFT... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextQt... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextSVG... Generating docs for compound RDKit::MolDraw2D_detail::LinePair... Generating docs for compound RDKit::MolDraw2D_detail::StringRect... Generating docs for namespace RDKit::MolDraw2DUtils Generating docs for compound RDKit::MolDraw2DUtils::ContourParams... Generating docs for namespace RDKit::MolEnumerator Generating docs for compound RDKit::MolEnumerator::LinkNode... Generating docs for compound RDKit::MolEnumerator::LinkNodeOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorParams... Generating docs for compound RDKit::MolEnumerator::PositionVariationOp... Generating docs for compound RDKit::MolEnumerator::RepeatUnitOp... Generating docs for namespace RDKit::MolEnumerator::detail Generating docs for namespace RDKit::MolEnumerator::utils Generating docs for namespace RDKit::MolFragmenter Generating docs for compound RDKit::MolFragmenter::FragmenterBondType... Generating docs for namespace RDKit::MolHash Generating docs for namespace RDKit::MolInterchange Generating docs for compound RDKit::MolInterchange::JSONParseParameters... Generating docs for compound RDKit::MolInterchange::JSONWriteParameters... Generating docs for namespace RDKit::MolOps Generating docs for compound RDKit::MolOps::AdjustQueryParameters... Generating docs for compound RDKit::MolOps::Hybridizations... Generating docs for compound RDKit::MolOps::RemoveHsParameters... Generating docs for namespace RDKit::MolOps::details Generating docs for namespace RDKit::MolProcessing Generating docs for namespace RDKit::MolProcessing::details Generating docs for namespace RDKit::MolShapes Generating docs for namespace RDKit::MolStandardize Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogEntry... Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogParams... Generating docs for compound RDKit::MolStandardize::AllowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::ChargeCorrection... Generating docs for compound RDKit::MolStandardize::CleanupParameters... Generating docs for compound RDKit::MolStandardize::CompositeValidation... Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::DisallowedRadicalValidation... Generating docs for compound RDKit::MolStandardize::FeaturesValidation... Generating docs for compound RDKit::MolStandardize::FragmentCatalogEntry... Generating docs for compound RDKit::MolStandardize::FragmentCatalogParams... Generating docs for compound RDKit::MolStandardize::FragmentRemover... Generating docs for compound RDKit::MolStandardize::FragmentValidation... Generating docs for compound RDKit::MolStandardize::Is2DValidation... Generating docs for compound RDKit::MolStandardize::IsotopeValidation... Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser... Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest... Generating docs for compound RDKit::MolStandardize::Layout2DValidation... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKit::MolStandardize::MetalDisconnectorOptions... Generating docs for compound RDKit::MolStandardize::MolVSValidation... Generating docs for compound RDKit::MolStandardize::NeutralValidation... Generating docs for compound RDKit::MolStandardize::NoAtomValidation... Generating docs for compound RDKit::MolStandardize::Normalizer... Generating docs for compound RDKit::MolStandardize::Pipeline... Generating docs for compound RDKit::MolStandardize::PipelineLogEntry... Generating docs for compound RDKit::MolStandardize::PipelineOptions... Generating docs for compound RDKit::MolStandardize:/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.h:204: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.h:204: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.h:204: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.h:262: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.h:262: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.h:262: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::MorganFingerprint::MorganAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganFingerprints.h:117: warning: The following parameter of RDKit::MorganFingerprints::getHashedFingerprint(const ROMol &mol, unsigned int radius, unsigned int nBits=2048, std::vector< boost::uint32_t > *invariants=nullptr, const std::vector< boost::uint32_t > *fromAtoms=nullptr, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=nullptr, bool includeRedundantEnvironments=false) is not documented: parameter 'nBits' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:26: warning: The following parameter of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<> > *atomTypes=nullptr) is not documented: parameter 'atomTypes' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesWrite.h:101: warning: argument 'bondIn' of command @param is not found in the argument list of RDKit::SmilesWrite::GetAtomSmiles(const Atom *atom, bool doKekule=false, const Bond *=nullptr, bool allHsExplicit=false, bool isomericSmiles=true) :PipelineResult... Generating docs for compound RDKit::MolStandardize::RDKitValidation... Generating docs for compound RDKit::MolStandardize::Reionizer... Generating docs for compound RDKit::MolStandardize::StereoValidation... Generating docs for compound RDKit::MolStandardize::Tautomer... Generating docs for compound RDKit::MolStandardize::TautomerCatalogEntry... Generating docs for compound RDKit::MolStandardize::TautomerCatalogParams... Generating docs for compound RDKit::MolStandardize::TautomerEnumerator... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorCallback... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorResult... Generating docs for nested compound RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator... Generating docs for compound RDKit::MolStandardize::TautomerTransform... Generating docs for compound RDKit::MolStandardize::TransformCatalogEntry... Generating docs for compound RDKit::MolStandardize::TransformCatalogParams... Generating docs for compound RDKit::MolStandardize::Uncharger... Generating docs for compound RDKit::MolStandardize::ValidationMethod... Generating docs for namespace RDKit::MolStandardize::defaults Generating docs for namespace RDKit::MolStandardize::Operations Generating docs for namespace RDKit::MolStandardize::TautomerScoringFunctions Generating docs for namespace RDKit::MorganFingerprint Generating docs for compound RDKit::MorganFingerprint::MorganArguments... Generating docs for compound RDKit::MorganFingerprint::MorganAtomEnv... Generating docs for compound RDKit::MorganFingerprint::MorganAtomInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganBondInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganEnvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator... Generating docs for namespace RDKit::MorganFingerprints Generating docs for compound RDKit::MorganFingerprints::ss_matcher... Generating docs for namespace RDKit::PicklerOps Generating docs for namespace RDKit::PNGData Generating docs for namespace RDKit::QueryOps Generating docs for namespace RDKit::RascalMCES Generating docs for compound RDKit::RascalMCES::PartitionSet... Generating docs for compound RDKit::RascalMCES::RascalClusterOptions... Generating docs for compound RDKit::RascalMCES::RascalOptions... Generating docs for compound RDKit::RascalMCES::RascalResult... Generating docs for namespace RDKit::RascalMCES::details Generating docs for compound RDKit::RascalMCES::details::ClusNode... Generating docs for namespace RDKit::RDKitFP Generating docs for compound RDKit::RDKitFP::RDKitFPArguments... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomEnv... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomInvGenerator... Generating docs for compound RDKit::RDKitFP::RDKitFPEnvGenerator... Generating docs for namespace RDKit::RDKitFPUtils Generating docs for namespace RDKit::RDTypeTag Generating docs for namespace RDKit::RDTypeTag::detail Generating docs for compound RDKit::RDTypeTag::detail::Value... Generating docs for namespace RDKit::ReactionRunnerUtils Generating docs for namespace RDKit::ReducedGraphs Generating docs for namespace RDKit::RxnOps Generating docs for namespace RDKit::ScaffoldNetwork Generating docs for compound RDKit::ScaffoldNetwork::NetworkEdge... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetwork... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetworkParams... Generating docs for namespace RDKit::ScaffoldNetwork::detail Generating docs for namespace RDKit::SGroupParsing Generating docs for namespace RDKit::SGroupWriting Generating docs for namespace RDKit::SLNParse Generating docs for compound RDKit::SLNParse::AttribType... Generating docs for namespace RDKit::SmartsWrite Generating docs for namespace RDKit::SmilesParse Generating docs for compound RDKit::SmilesParse::SmilesParseException... Generating docs for namespace RDKit::SmilesWrite Generating docs for namespace RDKit::SmilesWrite::detail Generating doc/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:94: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool includeChirality=false, uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=true, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:94: warning: The following parameter of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool includeChirality=false, uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=true, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false) is not documented: parameter 'countSimulation' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:32: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality, const uint32_t torsionAtomCount, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:32: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality, const uint32_t torsionAtomCount, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) is not documented: parameter 'countSimulation' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:68: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::TopologicalTorsionAtomEnv(OutputType bitId, INT_VECT atomPath) is not documented: parameter 'atomPath' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/CDXMLParser.h:95: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::v1::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/CDXMLParser.h:95: warning: The following parameter of RDKit::v1::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/FileParsers.h:76: warning: argument 'line' from the argument list of RDKit::v1::MolDataStreamToMol has multiple @param documentation sections /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/CDXMLParser.h:46: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::v2::CDXMLParser::MolsFromCDXMLFile(const std::string &filename, const CDXMLParserParams ¶ms=CDXMLParserParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/CDXMLParser.h:46: warning: The following parameter of RDKit::v2::CDXMLParser::MolsFromCDXMLFile(const std::string &filename, const CDXMLParserParams ¶ms=CDXMLParserParams()) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'removeHs' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'strictParsing' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: The following parameter of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'delimiter' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'smilesColumn' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'nameColumn' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'titleLine' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: The following parameter of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'nameRecord' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'confId2D' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'confId3D' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: The following parameter of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/HierarchicalClusterPicker.h:48: warning: The following parameter of RDPickers::HierarchicalClusterPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize) const is not documented: parameter 'distMat' /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/LeaderPicker.h:87: warning: The following parameters of RDPickers::LeaderPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize, const RDKit::INT_VECT &firstPicks, double threshold, int nthreads) const are not documented: parameter 'threshold' parameter 'nthreads' /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const s for namespace RDKit::StructureCheck Generating docs for compound RDKit::StructureCheck::AugmentedAtom... Generating docs for compound RDKit::StructureCheck::ChargeFix... Generating docs for compound RDKit::StructureCheck::IncEntry... Generating docs for compound RDKit::StructureCheck::Ligand... Generating docs for compound RDKit::StructureCheck::Neighbourhood... Generating docs for compound RDKit::StructureCheck::PathEntry... Generating docs for compound RDKit::StructureCheck::StructChecker... Generating docs for compound RDKit::StructureCheck::StructCheckerOptions... Generating docs for compound RDKit::StructureCheck::StructCheckTautomer... Generating docs for namespace RDKit::Subgraphs Generating docs for namespace RDKit::SubstanceGroupChecks Generating docs for namespace RDKit::TopologicalTorsion Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionArguments... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator... Generating docs for namespace RDKit::UFF Generating docs for namespace RDKit::UFF::Tools Generating docs for compound RDKit::UFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::Utils Generating docs for compound RDKit::Utils::LocaleSwitcher... Generating docs for namespace RDKit::Utils::detail Generating docs for namespace RDKit::v1 Generating docs for compound RDKit::v1::ForwardSDMolSupplier... Generating docs for compound RDKit::v1::MolSupplier... Generating docs for compound RDKit::v1::SDMolSupplier... Generating docs for compound RDKit::v1::SmartsParserParams... Generating docs for compound RDKit::v1::SmilesMolSupplier... Generating docs for compound RDKit::v1::SmilesParserParams... Generating docs for compound RDKit::v1::TDTMolSupplier... Generating docs for namespace RDKit::v2 Generating docs for namespace RDKit::v2::CDXMLParser Generating docs for compound RDKit::v2::CDXMLParser::CDXMLParserParams... Generating docs for namespace RDKit::v2::FileParsers Generating docs for compound RDKit::v2::FileParsers::ForwardSDMolSupplier... Generating docs for compound RDKit::v2::FileParsers::Mol2ParserParams... Generating docs for compound RDKit::v2::FileParsers::MolFileParserParams... Generating docs for compound RDKit::v2::FileParsers::MolFileUnhandledFeatureException... Generating docs for compound RDKit::v2::FileParsers::MolSupplier... Generating docs for compound RDKit::v2::FileParsers::PDBParserParams... Generating docs for compound RDKit::v2::FileParsers::SDMolSupplier... Generating docs for compound RDKit::v2::FileParsers::SmilesMolSupplier... Generating docs for compound RDKit::v2::FileParsers::SmilesMolSupplierParams... Generating docs for compound RDKit::v2::FileParsers::TDTMolSupplier... Generating docs for compound RDKit::v2::FileParsers::TDTMolSupplierParams... Generating docs for compound RDKit::v2::FileParsers::TPLParserParams... Generating docs for namespace RDKit::v2::MarvinParser Generating docs for compound RDKit::v2::MarvinParser::MrvParserParams... Generating docs for namespace RDKit::v2::ReactionParser Generating docs for namespace RDKit::v2::SmilesParse Generating docs for namespace RDLog Generating docs for namespace RDNumeric Generating docs for compound RDNumeric::Matrix... Generating docs for compound RDNumeric::SquareMatrix... Generating docs for compound RDNumeric::SymmMatrix... Generating docs for compound RDNumeric::Vector... Generating docs for namespace RDNumeric::Alignments Generating docs for namespace RDNumeric::EigenSolvers Generating docs for namespace RDPickers Generating docs for compound RDPickers::DistPicker... Generating docs for compound RDPickers::HierarchicalClusterPicker... Generating docs for compound RDPickers::LeaderPicker... Generating docs for compound RDPickers::LeaderPickerState... Generating docs for compound RDPickers::MaxMinPicker... Generating docs for compound RDPickers::MaxMinPickInfo... Generating docs for namespace RingUtils Generating docs for namespace SmilesParseOps Generating docs for namespace SmilesParseOps::detail Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... type lookup cache used 35633/65536 hits=212044 misses=39498 symbol lookup cache used 31373/65536 hits=284977 misses=31373 finished... (cd /build/reproducible-path/rdkit-202409.2/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202409.2 /usr/bin/make html) make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202409.2/Code/docs/* _build/html/cppapi cp -r C++Examples _build/html/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v8.1.3 loading translations [en]... done WARNING: html_static_path entry '_static' does not exist myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 260 source files that are out of date updating environment: [new config] 260 added, 0 changed, 0 removed reading sources... 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[100%] source/rdkit.utils.spiral /build/reproducible-path/rdkit-202409.2/Docs/Book/BackwardsIncompatibleChanges.md:49: WARNING: duplicate label changes to canonicalization, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/BackwardsIncompatibleChanges.md [autosectionlabel.BackwardsIncompatibleChanges] /build/reproducible-path/rdkit-202409.2/Docs/Book/Cartridge.md:732: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/BackwardsIncompatibleChanges.md [autosectionlabel.Cartridge] /build/reproducible-path/rdkit-202409.2/Docs/Book/Cookbook.rst:7: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Cartridge.md [autosectionlabel.Cookbook] /build/reproducible-path/rdkit-202409.2/Docs/Book/Cookbook.rst:10: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Cartridge.md [autosectionlabel.Cookbook] /build/reproducible-path/rdkit-202409.2/Docs/Book/Cookbook.rst:2539: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Cartridge.md [autosectionlabel.Cookbook] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md:3: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Cookbook.rst [autosectionlabel.GettingStartedInC++] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md:305: WARNING: duplicate label writing molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Cookbook.rst [autosectionlabel.GettingStartedInC++] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:12: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:30: WARNING: duplicate label reading single molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:104: WARNING: duplicate label reading sets of molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:208: WARNING: duplicate label writing molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:393: WARNING: duplicate label writing sets of molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:434: WARNING: duplicate label working with molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:438: WARNING: duplicate label looping over atoms and bonds, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:481: WARNING: duplicate label ring information, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:550: WARNING: duplicate label modifying molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:618: WARNING: duplicate label working with 2d molecules: generating depictions, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:668: WARNING: duplicate label working with 3d molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:794: WARNING: duplicate label preserving molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:850: WARNING: duplicate label drawing molecules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:1089: WARNING: duplicate label substructure searching, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:1154: WARNING: duplicate label stereochemistry in substructure matches, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:1192: WARNING: duplicate label atom map indices in smarts, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:3434: WARNING: duplicate label the sssr problem, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst:3842: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Cookbook.rst [autosectionlabel.GettingStartedInPython] /build/reproducible-path/rdkit-202409.2/Docs/Book/Install.md:430: WARNING: duplicate label recommended extras, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Install.md [autosectionlabel.Install] /build/reproducible-path/rdkit-202409.2/Docs/Book/Install.md:474: WARNING: duplicate label testing the build (optional, but recommended), other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Install.md [autosectionlabel.Install] /build/reproducible-path/rdkit-202409.2/Docs/Book/Install.md:479: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst [autosectionlabel.Install] /build/reproducible-path/rdkit-202409.2/Docs/Book/Overview.md:145: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Install.md [autosectionlabel.Overview] /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst:179: WARNING: duplicate label aromaticity, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst:385: WARNING: duplicate label dative bonds, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst:536: WARNING: duplicate label stereochemistry, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Cookbook.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst:1265: WARNING: duplicate label chemical features, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst:2465: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Cookbook.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst:2563: WARNING: duplicate label rdkit fingerprints, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/GettingStartedInPython.rst [autosectionlabel.RDKit_Book] /build/reproducible-path/rdkit-202409.2/Docs/Book/RDKit_Book.rst:2729: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/Overview.md [autosectionlabel.RDKit_Book] WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst:114: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Draw.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolStandardize.rst:6: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.MolStandardize] WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolStandardize.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.DataManip] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip] WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip.Metric] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.DataManip.Metric] WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Dbase.rst:17: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.ForceField] WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.Geometry] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ForceField.rst [autosectionlabel.source/rdkit.Geometry] WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst:18: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst:26: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202409.2/Docs/Book/data/README.md: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying downloadable files... [ 5%] C++Examples/example1.cpp copying downloadable files... [ 11%] C++Examples/example2.cpp copying downloadable files... [ 16%] C++Examples/example3.cpp copying downloadable files... [ 21%] C++Examples/example4.cpp copying downloadable files... [ 26%] C++Examples/example5.cpp copying downloadable files... [ 32%] C++Examples/example6.cpp copying downloadable files... [ 37%] C++Examples/example7.cpp copying downloadable files... [ 42%] C++Examples/example8.cpp copying downloadable files... [ 47%] C++Examples/example9.cpp copying downloadable files... [ 53%] ../Code/GraphMol/Bond.h copying downloadable files... [ 58%] C++Examples/example10.cpp copying downloadable files... [ 63%] C++Examples/CMakeLists.txt copying downloadable files... [ 68%] C++Examples/example11.cpp copying downloadable files... [ 74%] C++Examples/example12.cpp copying downloadable files... [ 79%] C++Examples/example13.cpp copying downloadable files... [ 84%] C++Examples/example17.cpp copying downloadable files... [ 89%] C++Examples/example14.cpp copying downloadable files... [ 95%] C++Examples/example15.cpp copying downloadable files... [100%] C++Examples/example16.cpp copying static files... Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/sphinxdoc.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 0%] BackwardsIncompatibleChanges writing output... [ 1%] Cartridge writing output... [ 1%] Cookbook writing output... [ 2%] GettingStartedInC++ writing output... [ 2%] GettingStartedInPython writing output... [ 2%] Install writing output... [ 3%] Overview writing output... [ 3%] RDKit_Book writing output... [ 3%] api-docs writing output... [ 4%] data/README writing output... [ 4%] index writing output... [ 5%] source/rdkit writing output... [ 5%] source/rdkit.Avalon writing output... [ 5%] source/rdkit.Avalon.pyAvalonTools writing output... [ 6%] source/rdkit.Chem writing output... [ 6%] source/rdkit.Chem.AllChem writing output... [ 7%] source/rdkit.Chem.AtomPairs writing output... [ 7%] source/rdkit.Chem.AtomPairs.Pairs writing output... [ 7%] source/rdkit.Chem.AtomPairs.Sheridan writing output... [ 8%] source/rdkit.Chem.AtomPairs.Torsions writing output... [ 8%] source/rdkit.Chem.AtomPairs.Utils writing output... [ 8%] source/rdkit.Chem.BRICS writing output... [ 9%] source/rdkit.Chem.BuildFragmentCatalog writing output... [ 9%] source/rdkit.Chem.ChemUtils writing output... [ 10%] source/rdkit.Chem.ChemUtils.AlignDepict writing output... 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The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.2/Docs/Book' (cd /build/reproducible-path/rdkit-202409.2/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202409.2 /usr/bin/make latexpdf) make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202409.2/Code/docs/* _build/html/cppapi sphinx-build -b latex -d _build/doctrees . _build/latex Running Sphinx v8.1.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist loading pickled environment... done myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 248 changed, 0 removed reading sources... 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[100%] source/rdkit.utils.spiral WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst:24: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.utils.rst [autosectionlabel.source/rdkit] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst:36: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.utils.rst [autosectionlabel.source/rdkit] WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon] WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst:114: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem] WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils] WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Draw.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw] WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState] WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features] WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints] WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle] WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb] WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey] WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D] WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds] WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum] WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape] WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers] WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs] WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.DataManip] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip] WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip.Metric] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.DataManip.Metric] WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs] WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Dbase.rst:17: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase] WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry] WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.ForceField] WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.Geometry] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ForceField.rst [autosectionlabel.source/rdkit.Geometry] WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst:18: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst:26: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML] WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster] WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data] WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors] WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils] WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT] WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring] WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics] WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters] WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib] WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.2/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils] WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202409.2/Docs/Book/data/README.md: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/make.bat Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/Makefile Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/latexmkrc Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/latexmkjarc done copying assets: done processing RDKit.tex... index Overview Install GettingStartedInPython RDKit_Book Cookbook Cartridge BackwardsIncompatibleChanges api-docs source/rdkit source/rdkit.Avalon source/rdkit.Avalon.pyAvalonTools source/rdkit.Chem source/rdkit.Chem.AtomPairs source/rdkit.Chem.AtomPairs.Pairs source/rdkit.Chem.AtomPairs.Sheridan source/rdkit.Chem.AtomPairs.Torsions source/rdkit.Chem.AtomPairs.Utils source/rdkit.Chem.ChemUtils source/rdkit.Chem.ChemUtils.AlignDepict source/rdkit.Chem.ChemUtils.BulkTester source/rdkit.Chem.ChemUtils.DescriptorUtilities source/rdkit.Chem.ChemUtils.SDFToCSV source/rdkit.Chem.ChemUtils.TemplateExpand source/rdkit.Chem.Draw source/rdkit.Chem.Draw.IPythonConsole source/rdkit.Chem.Draw.MolDrawing source/rdkit.Chem.Draw.SimilarityMaps source/rdkit.Chem.Draw.rdMolDraw2D source/rdkit.Chem.Draw.rdMolDraw2DQt source/rdkit.Chem.EState source/rdkit.Chem.EState.AtomTypes source/rdkit.Chem.EState.EState source/rdkit.Chem.EState.EState_VSA source/rdkit.Chem.EState.Fingerprinter source/rdkit.Chem.FeatMaps source/rdkit.Chem.FeatMaps.FeatMapParser source/rdkit.Chem.FeatMaps.FeatMapPoint source/rdkit.Chem.FeatMaps.FeatMapUtils source/rdkit.Chem.FeatMaps.FeatMaps source/rdkit.Chem.Features source/rdkit.Chem.Features.FeatDirUtilsRD source/rdkit.Chem.Features.ShowFeats source/rdkit.Chem.Fingerprints source/rdkit.Chem.Fingerprints.ClusterMols source/rdkit.Chem.Fingerprints.DbFpSupplier source/rdkit.Chem.Fingerprints.FingerprintMols source/rdkit.Chem.Fingerprints.MolSimilarity source/rdkit.Chem.Fingerprints.SimilarityScreener source/rdkit.Chem.Fraggle source/rdkit.Chem.Fraggle.FraggleSim source/rdkit.Chem.MolDb source/rdkit.Chem.MolDb.FingerprintUtils source/rdkit.Chem.MolDb.Loader source/rdkit.Chem.MolDb.Loader_orig source/rdkit.Chem.MolDb.Loader_sa source/rdkit.Chem.MolKey source/rdkit.Chem.MolKey.InchiInfo source/rdkit.Chem.MolKey.MolKey source/rdkit.Chem.Pharm2D source/rdkit.Chem.Pharm2D.Generate source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D source/rdkit.Chem.Pharm2D.Matcher source/rdkit.Chem.Pharm2D.SigFactory source/rdkit.Chem.Pharm2D.Utils source/rdkit.Chem.Pharm3D source/rdkit.Chem.Pharm3D.EmbedLib source/rdkit.Chem.Pharm3D.ExcludedVolume source/rdkit.Chem.Pharm3D.Pharmacophore source/rdkit.Chem.Scaffolds source/rdkit.Chem.Scaffolds.MurckoScaffold source/rdkit.Chem.Scaffolds.rdScaffoldNetwork source/rdkit.Chem.SimpleEnum source/rdkit.Chem.SimpleEnum.Enumerator source/rdkit.Chem.Subshape source/rdkit.Chem.Subshape.BuilderUtils source/rdkit.Chem.Subshape.SubshapeAligner source/rdkit.Chem.Subshape.SubshapeBuilder source/rdkit.Chem.Subshape.SubshapeObjects source/rdkit.Chem.Suppliers source/rdkit.Chem.Suppliers.DbMolSupplier source/rdkit.Chem.Suppliers.MolSupplier source/rdkit.Chem.fmcs source/rdkit.Chem.fmcs.fmcs source/rdkit.Chem.AllChem source/rdkit.Chem.BRICS source/rdkit.Chem.BuildFragmentCatalog source/rdkit.Chem.ChemicalFeatures source/rdkit.Chem.ChemicalForceFields source/rdkit.Chem.Crippen source/rdkit.Chem.Descriptors source/rdkit.Chem.Descriptors3D source/rdkit.Chem.EnumerateHeterocycles source/rdkit.Chem.EnumerateStereoisomers source/rdkit.Chem.FastSDMolSupplier source/rdkit.Chem.FeatFinderCLI source/rdkit.Chem.FilterCatalog source/rdkit.Chem.FragmentCatalog source/rdkit.Chem.FragmentMatcher source/rdkit.Chem.Fragments source/rdkit.Chem.FunctionalGroups source/rdkit.Chem.GraphDescriptors source/rdkit.Chem.Graphs source/rdkit.Chem.Lipinski source/rdkit.Chem.MACCSkeys source/rdkit.Chem.MolCatalog source/rdkit.Chem.MolStandardize source/rdkit.Chem.MolStandardize.rdMolStandardize source/rdkit.Chem.MolSurf source/rdkit.Chem.PandasTools source/rdkit.Chem.PeriodicTable source/rdkit.Chem.PropertyMol source/rdkit.Chem.PyMol source/rdkit.Chem.QED source/rdkit.Chem.Randomize source/rdkit.Chem.Recap source/rdkit.Chem.ReducedGraphs source/rdkit.Chem.RegistrationHash source/rdkit.Chem.SATIS source/rdkit.Chem.SaltRemover source/rdkit.Chem.ShowMols source/rdkit.Chem.SpacialScore source/rdkit.Chem.TemplateAlign source/rdkit.Chem.TorsionFingerprints source/rdkit.Chem.inchi source/rdkit.Chem.rdchem source/rdkit.Chem.rdDistGeom source/rdkit.Chem.rdqueries source/rdkit.Chem.rdFMCS source/rdkit.Chem.rdMolAlign source/rdkit.Chem.rdMolHash source/rdkit.Chem.rdReducedGraphs source/rdkit.Chem.rdtrajectory source/rdkit.Chem.rdMolTransforms source/rdkit.Chem.rdmolfiles source/rdkit.Chem.rdPartialCharges source/rdkit.Chem.rdMolCatalog source/rdkit.Chem.rdCoordGen source/rdkit.Chem.rdMolChemicalFeatures source/rdkit.Chem.rdMMPA source/rdkit.Chem.rdRGroupDecomposition source/rdkit.Chem.rdForceFieldHelpers source/rdkit.Chem.rdDepictor source/rdkit.Chem.rdChemicalFeatures source/rdkit.Chem.rdmolops source/rdkit.Chem.rdFreeSASA source/rdkit.Chem.rdMolInterchange source/rdkit.Chem.rdShapeHelpers source/rdkit.Chem.rdinchi source/rdkit.Chem.rdChemReactions source/rdkit.Chem.rdSubstructLibrary source/rdkit.Chem.rdfiltercatalog source/rdkit.Chem.rdfragcatalog source/rdkit.Chem.rdMolDescriptors source/rdkit.Chem.rdFingerprintGenerator source/rdkit.Chem.rdMHFPFingerprint source/rdkit.Chem.rdSLNParse source/rdkit.Chem.rdAbbreviations source/rdkit.Chem.rdDeprotect source/rdkit.Chem.rdMolEnumerator source/rdkit.Chem.rdCIPLabeler source/rdkit.Chem.rdTautomerQuery source/rdkit.Chem.rdEHTTools source/rdkit.Chem.rdDetermineBonds source/rdkit.Chem.rdShapeAlign source/rdkit.DataManip source/rdkit.DataManip.Metric source/rdkit.DataManip.Metric.rdMetricMatrixCalc source/rdkit.DataStructs source/rdkit.DataStructs.BitEnsemble source/rdkit.DataStructs.BitEnsembleDb source/rdkit.DataStructs.BitUtils source/rdkit.DataStructs.LazySignature source/rdkit.DataStructs.TopNContainer source/rdkit.DataStructs.VectCollection source/rdkit.DataStructs.cDataStructs source/rdkit.Dbase source/rdkit.Dbase.DbConnection source/rdkit.Dbase.DbInfo source/rdkit.Dbase.DbModule source/rdkit.Dbase.DbResultSet source/rdkit.Dbase.DbUtils source/rdkit.Dbase.StorageUtils source/rdkit.DistanceGeometry source/rdkit.DistanceGeometry.DistGeom source/rdkit.ForceField source/rdkit.ForceField.rdForceField source/rdkit.Geometry source/rdkit.Geometry.rdGeometry source/rdkit.ML source/rdkit.ML.Cluster source/rdkit.ML.Cluster.Butina source/rdkit.ML.Cluster.ClusterUtils source/rdkit.ML.Cluster.ClusterVis source/rdkit.ML.Cluster.Clusters source/rdkit.ML.Cluster.Murtagh source/rdkit.ML.Cluster.Resemblance source/rdkit.ML.Cluster.Standardize source/rdkit.ML.Cluster.Clustering source/rdkit.ML.Data source/rdkit.ML.Data.DataUtils source/rdkit.ML.Data.FindQuantBounds source/rdkit.ML.Data.MLData source/rdkit.ML.Data.Quantize source/rdkit.ML.Data.cQuantize source/rdkit.ML.Data.SplitData source/rdkit.ML.Data.Stats source/rdkit.ML.Data.Transforms source/rdkit.ML.Descriptors source/rdkit.ML.Descriptors.CompoundDescriptors source/rdkit.ML.Descriptors.Descriptors source/rdkit.ML.Descriptors.MoleculeDescriptors source/rdkit.ML.Descriptors.Parser source/rdkit.ML.InfoTheory source/rdkit.ML.InfoTheory.BitClusterer source/rdkit.ML.InfoTheory.BitRank source/rdkit.ML.InfoTheory.entropy source/rdkit.ML.InfoTheory.rdInfoTheory source/rdkit.ML.MLUtils source/rdkit.ML.MLUtils.VoteImg source/rdkit.ML.SLT source/rdkit.ML.SLT.Risk source/rdkit.ML.Scoring source/rdkit.ML.Scoring.Scoring source/rdkit.ML.MatOps source/rdkit.ML.files source/rdkit.Numerics source/rdkit.Numerics.rdAlignment source/rdkit.SimDivFilters source/rdkit.SimDivFilters.SimilarityPickers source/rdkit.SimDivFilters.rdSimDivPickers source/rdkit.VLib source/rdkit.VLib.NodeLib source/rdkit.VLib.NodeLib.DbMolSupply source/rdkit.VLib.NodeLib.DbPickleSupplier source/rdkit.VLib.NodeLib.SDSupply source/rdkit.VLib.NodeLib.SmartsMolFilter source/rdkit.VLib.NodeLib.SmartsRemover source/rdkit.VLib.NodeLib.SmilesDupeFilter source/rdkit.VLib.NodeLib.SmilesOutput source/rdkit.VLib.NodeLib.SmilesSupply source/rdkit.VLib.Filter source/rdkit.VLib.Node source/rdkit.VLib.Output source/rdkit.VLib.Supply source/rdkit.VLib.Transform source/rdkit.utils source/rdkit.utils.cactvs source/rdkit.utils.chemutils source/rdkit.utils.fileutils source/rdkit.utils.listutils source/rdkit.utils.spiral source/rdkit.rdBase source/rdkit.RDConfig source/rdkit.RDLogger source/rdkit.RDPaths source/rdkit.RDRandom source/rdkit.TestRunner GettingStartedInC++ resolving references... 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[1] [2] Chapter 1. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) [2] [3] [4] Chapter 2. [5] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [6] [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 774--776 []\T1/qtm/m/n/10 If you want to use the python wrap-pers: \T1/txtt/m/n/10 ./boo tstrap.sh [][]with[]libraries=python, [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 941--943 []\T1/qtm/m/n/10 You can en-able sup-port for gen-er-at-ing InChI strings and I nChI keys by adding the ar-gu-ment [11] [12] Underfull \hbox (badness 5490) in paragraph at lines 1166--1168 \T1/qtm/m/n/10 This sec-tion as-sumes that python is in-stalled in \T1/txtt/m/n /10 C:[]Python36 that the boost libraries have been [13] Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\T1/txtt/m/n/10 DBOOST_ROOT=C:/boost []DRDK_BUILD_INCHI_SUPPORT=ON []DRDK_BUI LD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\T1/txtt/m/n/10 DRDK_BUILD_PGSQL=ON []DPostgreSQL_ROOT="C:[]Program Files[]Po stgreSQL[]9.5" []G"Visual Underfull \hbox (badness 10000) in paragraph at lines 1231--1233 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] Underfull \hbox (badness 10000) in paragraph at lines 1239--1241 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] [14] Chapter 3. [15] [16 <./Cc1ccccc1.png>] [17] [18] LaTeX Warning: Hyper reference `GettingStartedInPython:chem-vs-allchem' on page 19 undefined on input line 1584. [19] [20] [21] [22] LaTeX Warning: Hyper reference `GettingStartedInPython:the-sssr-problem' on pag e 23 undefined on input line 1824. [23] [24] Underfull \hbox (badness 10000) in paragraph at lines 1974--1977 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1974--1977 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 1999--2005 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. [25 <./picture_1.png (PNG copy)> <./picture_0.png (PNG copy)> <./picture_3.png (PNG copy)> <./picture_2.png> <./picture_4.png>] [26] [27] [28] [29 <./cdk2_mol1.png> <./cdk2_mol2.png> <./cdk2_molgrid.png (PNG copy)>] [30 <./cdk2_molgrid_aligned.png (PNG copy)>] [31 <./atom_highlights_1.png>] [32 <./atom_highlights_2.png> <./atom_highlights_3.png>] Overfull \vbox (1.98868pt too high) detected at line 2451 [33 <./atom_annotation_1.png> <./atom_labels_1.png>] [34 <./atom_labels_2.png>] [35 <./atom_labels_3.png> <./mol_metadata1.png>] [36] LaTeX Warning: Hyper reference `GettingStartedInPython:chemical-reactions' on p age 37 undefined on input line 2647. [37] Overfull \vbox (2.6316pt too high) detected at line 2739 [38{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}] [39 <./substruct_search_parameters1.png>] LaTeX Warning: Hyper reference `GettingStartedInPython:chemical-reactions' on p age 40 undefined on input line 2786. [40] [41] [42 <./mcs_example_1.png> <./mcs_example_2.png>] [43 <./mcs_example_3.png> <./mcs_example_4.png>] [44 <./mcs_example_5.png> <./mcs_example_6.png>] [45] [46] [47] [48] [49] [50] LaTeX Warning: Hyper reference `GettingStartedInPython:feature-definitions-used -in-the-morgan-fingerprints' on page 51 undefined on input line 3496. [51] [52] [53] [54] [55 <./mfp2_bit872.png> <./rdk_bit1553.png>] [56 <./rdk_bit1553_2.png>] [57] [58 <./similarity_map_fp1.png>] [59 <./similarity_map_fp2.png>] LaTeX Warning: Hyper reference `GettingStartedInPython:list-of-available-descri ptors' on page 60 undefined on input line 4004. Overfull \vbox (1.67828pt too high) detected at line 4017 [60 <./similarity_map_fp3.png>] [61] [62 <./similarity_map_charges.png>] LaTeX Warning: Hyper reference `RDKit_Book::doc' on page 63 undefined on input line 4113. 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[103 <./nontetstereo_oh2.png> <./nontetstereo_oh1.png>] Underfull \hbox (badness 10000) in paragraph at lines 9443--9445 []\T1/qtm/m/n/10 The clas-sic ex-am-ple of this is cis-platin - \T1/txtt/m/n/10 Cl[Pt@SP1](Cl)(<[][NH3])<[][NH3] \T1/qtm/m/n/10 - vs trans-platin - [104 <./nontetstereo_ex1.png> <./nontetstereo_ex2.png> <./nontetstereo_missing1 .png>] [105] [106] [107] [108] [109] [110] LaTeX Warning: Hyper reference `RDKit_Book:ph4-figure' on page 111 undefined on input line 10000. [111] [112 <./picture_10.jpg>] Overfull \vbox (2.86082pt too high) detected at line 10266 [113] Package longtable Warning: Column widths have changed (longtable) in table 3 on input line 10579. [114 <./ary_group.png>] [115] [116] Underfull \hbox (badness 10000) in paragraph at lines 10901--10903 \T1/qtm/m/n/10 Here's the rd-kitj-son rep-re-sen-ta-tion of the stereo groups f rom the molecule [117] Underfull \hbox (badness 10000) in paragraph at lines 11139--11139 []\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 11139--11139 []\T1/qtm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 11139--11139 []\T1/qtm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 11139--11139 []\T1/qtm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 11139--11139 []\T1/qtm/m/n/10 mol-Rxn-Com-po- [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 11301--11306 []\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. [120] Underfull \hbox (badness 10000) in paragraph at lines 11350--11353 []\T1/qtm/m/n/10 This be-hav-ior is en-abled by de-fault and can be turned on/o ff with the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 10000) in paragraph at lines 11354--11358 \T1/qtm/m/n/10 tions \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.CreateAtomStringProp ertyList()\T1/qtm/m/n/10 , \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. [121] Underfull \hbox (badness 10000) in paragraph at lines 11498--11498 []\T1/qhv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 11498--11498 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 11498--11498 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 11498--11498 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 11498--11498 []\T1/qtm/m/n/10 mix- [122] [123 <./enhanced_stereo_and1_and2_base.png> <./enhanced_stereo_and1_and2_expand .png> <./enhanced_stereo_and1_cis_base.png> <./enhanced_stereo_and1_cis_expand. png> <./enhanced_stereo_and1_trans_base.png> <./enhanced_stereo_and1_trans_expa nd.png> <./enhanced_stereo_or1_or2_base.png> <./enhanced_stereo_or1_cis_base.pn g> <./enhanced_stereo_or1_trans_base.png> <./enhanced_stereo_abs_and_base.png> <./enhanced_stereo_abs_and_expand.png> <./enhanced_stereo_abs_or_base.png>] Underfull \hbox (badness 10000) in paragraph at lines 11515--11520 []\T1/qtm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/txtt/m /n/10 StereoGroup \T1/qtm/m/n/10 us-ing the func-tion \T1/txtt/m/n/10 rdkit.Che m. [124] [125 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./EnhancedS tereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_molE.png > <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [126] [127 <./atrop_example1.png> <./atrop_example2.png> <./atrop_example3.png>] [128 <./atrop_representation1.png>] [129 <./atrop_example4.png>] [130 <./atrop_example5.png> <./atrop_representation2.png>] [131 <./query_bonds.png>] [132 <./query_bonds.2.png> <./query_atoms.png>] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 []\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1 /txtt/m/n/10 true \T1/qtm/m/n/10 non-tetrahedral chi-ral-ity will be per- Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/qtm/m/n/10 ceived from 3D co-or-di-nates. The de-fault value is \T1/txtt/m/ n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-ment vari- Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/qtm/m/n/10 able \T1/txtt/m/n/10 RDK_ENABLE_NONTETRAHEDRAL_STEREO \T1/qtm/m/ n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked from Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA llowNontetrahedralChirality() \T1/qtm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n /10 or from Python us-ing the func-tions Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 []\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per- Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is \T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION \T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality: :setUseLegacyStereoPerception() \T1/qtm/m/n/10 / [135] [136] Chapter 5. [137] [138 <./RDKitCB_0_im0.png> <./RDKitCB_0_im1.png>] [139 <./RDKitCB_0_im2.png> <./RDKitCB_40_im0.png>] [140 <./RDKitCB_40_im1.png> <./RDKitCB_23_im0.png>] [141 <./RDKitCB_23_im1.png> <./RDKitCB_32_im0.png>] [142 <./RDKitCB_32_im1.png> <./RDKitCB_1_im0.png (PNG copy)>] [143 <./RDKitCB_1_im1.png (PNG copy)> <./RDKitCB_1_im2.png (PNG copy)>] [144 <./RDKitCB_1_im3.png (PNG copy)> <./RDKitCB_2_im0.png>] [145 <./RDKitCB_2_im1.png> <./RDKitCB_36_im0.png>] [146 <./RDKitCB_36_im1.png>] [147 <./RDKitCB_38_im0.png>] [148 <./RDKitCB_39_im0.png (PNG copy)>] [149 <./RDKitCB_17_im0.png> <./RDKitCB_17_im1.png>] [150 <./RDKitCB_34_im0.png> <./RDKitCB_34_im1.png> <./RDKitCB_34_im2.png>] [151] Overfull \hbox (396.49246pt too wide) in paragraph at lines 13270--13270 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [152 <./RDKitCB_37_im0.png>] Overfull \hbox (396.49246pt too wide) in paragraph at lines 13299--13299 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [153 <./RDKitCB_37_im1.png>] [154 <./RDKitCB_37_im2.png>] [155 <./RDKitCB_35_im0.png>] [156] [157 <./RDKitCB_3_im0.png> <./RDKitCB_8_im0.png>] [158] [159 <./RDKitCB_30_im0.png>] [160 <./RDKitCB_30_im1.png>] [161 <./RDKitCB_7_im0.png> <./RDKitCB_7_im1.png>] [162 <./RDKitCB_7_im2.png (PNG copy)> <./RDKitCB_7_im3.png> <./RDKitCB_7_im4.pn g>] [163 <./RDKitCB_7_im5.png> <./RDKitCB_7_im6.png (PNG copy)>] [164] [165] [166 <./RDKitCB_29_im0.png (PNG copy)>] Underfull \vbox (badness 1043) detected at line 13953 [167 <./RDKitCB_33_im0.png (PNG copy)>] Overfull \vbox (0.99814pt too high) detected at line 13988 [168 <./RDKitCB_33_im1.png (PNG copy)>] [169 <./RDKitCB_33_im2.png (PNG copy)>] Overfull \hbox (490.99219pt too wide) in paragraph at lines 14054--14054 []\T1/txtt/m/n/10 "[][]CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C @H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@ @H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O[][] [170 <./RDKitCB_13_im0.png>] [171 <./RDKitCB_13_im1.png>] [172] [173 <./RDKitCB_20_im0.png>] [174 <./RDKitCB_21_im0.png>] [175 <./RDKitCB_21_im1.png>] [176 <./RDKitCB_21_im2.png (PNG copy)> <./RDKitCB_21_im3.png>] [177 <./RDKitCB_21_im4.png>] [178 <./RDKitCB_21_im5.png (PNG copy)>] [179 <./RDKitCB_22_im0.png>] [180 <./RDKitCB_22_im1.png>] [181 <./RDKitCB_6_im0.png (PNG copy)>] [182 <./RDKitCB_6_im1.png (PNG copy)> <./RDKitCB_6_im2.png (PNG copy)>] [183] [184] [185] [186] [187 <./RDKitCB_19_im0.png>] [188] [189] [190 <./RDKitCB_28_im0.png (PNG copy)> <./RDKitCB_28_im1.png (PNG copy)>] [191] [192] Chapter 6. [193] [194] [195] [196] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 15554--15554 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 15556--15556 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 15557--15557 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 15558--15558 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (464.74226pt too wide) in paragraph at lines 15559--15559 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC(=O)NC(C)(C)C(=O)NC( Cc1ccccc1)C(=O)NC(CC(C)C)C(=O)NC(Cc1ccccc1)C(=O)NC(CCCNC(=N)N)C(=O)N1CCCC1C(=O) NC(CCCNC(=N)N)C(=O)NC(CC(N)=O)C(N)=O| Overfull \hbox (359.74257pt too wide) in paragraph at lines 15560--15560 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 15561--15561 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 15562--15562 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 15563--15563 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \vbox (2.3893pt too high) detected at line 15565 [197] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 15577--15577 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 15579--15579 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 15580--15580 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 15581--15581 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (359.74257pt too wide) in paragraph at lines 15582--15582 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 15583--15583 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 15584--15584 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 15585--15585 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \hbox (522.4921pt too wide) in paragraph at lines 15586--15586 []\T1/txtt/m/n/10 CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@H] (C(=O)N1CCC[C@H]1C(=O)N1CCC[C@H]1C(=O)N[C@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CC(C )C)C(=O)O)Cc1ccccc1)Cc1ccccc1)C(C)C)[C@@H](C)CC| [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] Chapter 7. [213] [214] [215] Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [216] [217] [218] Chapter 8. [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] Chapter 9. [231] [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 18704--18708 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [234] [235] [236] [237] [238] Overfull \vbox (0.8796pt too high) detected at line 19141 [239] [240] Underfull \hbox (badness 6691) in paragraph at lines 19244--19246 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [241] [242] LaTeX Warning: Hyper reference `GettingStartedInC++:the-sssr-problem' on page 2 43 undefined on input line 19372. LaTeX Warning: Hyper reference `GettingStartedInC++:two-add-hs' on page 243 und efined on input line 19402. [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] Overfull \vbox (1.8739pt too high) detected at line 20261 [253] [254] [255] [256] Chapter 10. [257] [258] Chapter 11. No file RDKit.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. [259] (./RDKit.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `RDKit.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on RDKit.pdf (263 pages, 2863468 bytes). Transcript written on RDKit.log. Latexmk: Missing input file 'RDKit.toc' (or dependence on it) from following: No file RDKit.toc. Latexmk: Missing input file 'RDKit.ind' (or dependence on it) from following: No file RDKit.ind. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'RDKit.pdf' Have index file 'RDKit.idx', RDKit.ind RDKit Latexmk: applying rule 'makeindex RDKit.idx'... Rule 'makeindex RDKit.idx': Reasons for rerun Category 'other': Rerun of 'makeindex RDKit.idx' forced or previously required: Reason or flag: 'Initial set up of rule' ------------ Run number 1 of rule 'makeindex RDKit.idx' ------------ ------------ Running 'makeindex -s python.ist -o "RDKit.ind" "RDKit.idx"' ------------ This is makeindex, version 2.17 [TeX Live 2025/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file RDKit.idx...done (0 entries accepted, 0 rejected). Nothing written in RDKit.ind. Transcript written in RDKit.ilg. Latexmk: applying rule 'pdflatex'... Rule 'pdflatex': Reasons for rerun Changed files or newly in use/created: RDKit.aux RDKit.ind RDKit.out RDKit.toc ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "RDKit.tex"' ------------ This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./RDKit.tex LaTeX2e <2024-11-01> L3 programming layer <2024-11-02> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}] [2] [3] [4] Chapter 2. 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[15] [16 <./Cc1ccccc1.png>] [17] [18] [19] [20] [21] [22] [23] [24] Underfull \hbox (badness 10000) in paragraph at lines 1974--1977 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1974--1977 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 1999--2005 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. 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[124] [125 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./EnhancedS tereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_molE.png > <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [126] [127 <./atrop_example1.png> <./atrop_example2.png> <./atrop_example3.png>] [128 <./atrop_representation1.png>] [129 <./atrop_example4.png>] [130 <./atrop_example5.png> <./atrop_representation2.png>] [131 <./query_bonds.png>] [132 <./query_bonds.2.png> <./query_atoms.png>] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 []\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1 /txtt/m/n/10 true \T1/qtm/m/n/10 non-tetrahedral chi-ral-ity will be per- Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/qtm/m/n/10 ceived from 3D co-or-di-nates. 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Can set/checked from Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA llowNontetrahedralChirality() \T1/qtm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n /10 or from Python us-ing the func-tions Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 []\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per- Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is \T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION \T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality: :setUseLegacyStereoPerception() \T1/qtm/m/n/10 / [135] [136] Chapter 5. [137] [138 <./RDKitCB_0_im0.png> <./RDKitCB_0_im1.png>] [139 <./RDKitCB_0_im2.png> <./RDKitCB_40_im0.png>] [140 <./RDKitCB_40_im1.png> <./RDKitCB_23_im0.png>] [141 <./RDKitCB_23_im1.png> <./RDKitCB_32_im0.png>] [142 <./RDKitCB_32_im1.png> <./RDKitCB_1_im0.png (PNG copy)>] [143 <./RDKitCB_1_im1.png (PNG copy)> <./RDKitCB_1_im2.png (PNG copy)>] [144 <./RDKitCB_1_im3.png (PNG copy)> <./RDKitCB_2_im0.png>] [145 <./RDKitCB_2_im1.png> <./RDKitCB_36_im0.png>] [146 <./RDKitCB_36_im1.png>] [147 <./RDKitCB_38_im0.png>] [148 <./RDKitCB_39_im0.png (PNG copy)>] [149 <./RDKitCB_17_im0.png> <./RDKitCB_17_im1.png>] [150 <./RDKitCB_34_im0.png> <./RDKitCB_34_im1.png> <./RDKitCB_34_im2.png>] [151] Overfull \hbox (396.49246pt too wide) in paragraph at lines 13270--13270 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [152 <./RDKitCB_37_im0.png>] Overfull \hbox (396.49246pt too wide) in paragraph at lines 13299--13299 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [153 <./RDKitCB_37_im1.png>] [154 <./RDKitCB_37_im2.png>] [155 <./RDKitCB_35_im0.png>] [156] [157 <./RDKitCB_3_im0.png> <./RDKitCB_8_im0.png>] [158] [159 <./RDKitCB_30_im0.png>] [160 <./RDKitCB_30_im1.png>] [161 <./RDKitCB_7_im0.png> <./RDKitCB_7_im1.png>] [162 <./RDKitCB_7_im2.png (PNG copy)> <./RDKitCB_7_im3.png> <./RDKitCB_7_im4.pn g>] [163 <./RDKitCB_7_im5.png> <./RDKitCB_7_im6.png (PNG copy)>] [164] [165] [166 <./RDKitCB_29_im0.png (PNG copy)>] Underfull \vbox (badness 1043) detected at line 13953 [167 <./RDKitCB_33_im0.png (PNG copy)>] Overfull \vbox (0.99814pt too high) detected at line 13988 [168 <./RDKitCB_33_im1.png (PNG copy)>] [169 <./RDKitCB_33_im2.png (PNG copy)>] Overfull \hbox (490.99219pt too wide) in paragraph at lines 14054--14054 []\T1/txtt/m/n/10 "[][]CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C @H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@ @H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O[][] [170 <./RDKitCB_13_im0.png>] [171 <./RDKitCB_13_im1.png>] [172] [173 <./RDKitCB_20_im0.png>] [174 <./RDKitCB_21_im0.png>] [175 <./RDKitCB_21_im1.png>] [176 <./RDKitCB_21_im2.png (PNG copy)> <./RDKitCB_21_im3.png>] [177 <./RDKitCB_21_im4.png>] [178 <./RDKitCB_21_im5.png (PNG copy)>] [179 <./RDKitCB_22_im0.png>] [180 <./RDKitCB_22_im1.png>] [181 <./RDKitCB_6_im0.png (PNG copy)>] [182 <./RDKitCB_6_im1.png (PNG copy)> <./RDKitCB_6_im2.png (PNG copy)>] [183] [184] [185] [186] [187 <./RDKitCB_19_im0.png>] [188] [189] [190 <./RDKitCB_28_im0.png (PNG copy)> <./RDKitCB_28_im1.png (PNG copy)>] [191] [192] Chapter 6. [193] [194] [195] [196] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 15554--15554 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 15556--15556 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 15557--15557 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 15558--15558 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (464.74226pt too wide) in paragraph at lines 15559--15559 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC(=O)NC(C)(C)C(=O)NC( Cc1ccccc1)C(=O)NC(CC(C)C)C(=O)NC(Cc1ccccc1)C(=O)NC(CCCNC(=N)N)C(=O)N1CCCC1C(=O) NC(CCCNC(=N)N)C(=O)NC(CC(N)=O)C(N)=O| Overfull \hbox (359.74257pt too wide) in paragraph at lines 15560--15560 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 15561--15561 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 15562--15562 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 15563--15563 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \vbox (2.3893pt too high) detected at line 15565 [197] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 15577--15577 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 15579--15579 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 15580--15580 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 15581--15581 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (359.74257pt too wide) in paragraph at lines 15582--15582 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 15583--15583 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 15584--15584 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 15585--15585 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \hbox (522.4921pt too wide) in paragraph at lines 15586--15586 []\T1/txtt/m/n/10 CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@H] (C(=O)N1CCC[C@H]1C(=O)N1CCC[C@H]1C(=O)N[C@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CC(C )C)C(=O)O)Cc1ccccc1)Cc1ccccc1)C(C)C)[C@@H](C)CC| [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] Chapter 7. [213] [214] [215] Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [216] [217] [218] Chapter 8. [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] Chapter 9. [231] [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 18704--18708 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [234] [235] [236] [237] [238] Overfull \vbox (0.8796pt too high) detected at line 19141 [239] [240] Underfull \hbox (badness 6691) in paragraph at lines 19244--19246 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] Overfull \vbox (1.8739pt too high) detected at line 20261 [253] [254] [255] [256] Chapter 10. [257] [258] Chapter 11. (./RDKit.ind) [259] (./RDKit.aux) ) (see the transcript file for additional information) Output written on RDKit.pdf (269 pages, 2935735 bytes). Transcript written on RDKit.log. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Have index file 'RDKit.idx', RDKit.ind RDKit Latexmk: applying rule 'pdflatex'... Rule 'pdflatex': Reasons for rerun Changed files or newly in use/created: RDKit.aux ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "RDKit.tex"' ------------ This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./RDKit.tex LaTeX2e <2024-11-01> L3 programming layer <2024-11-02> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 131--133 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}] [2] [3] [4] Chapter 2. 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[15] [16 <./Cc1ccccc1.png>] [17] [18] [19] [20] [21] [22] [23] [24] Underfull \hbox (badness 10000) in paragraph at lines 1974--1977 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1974--1977 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 1999--2005 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. 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[124] [125 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./EnhancedS tereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_molE.png > <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [126] [127 <./atrop_example1.png> <./atrop_example2.png> <./atrop_example3.png>] [128 <./atrop_representation1.png>] [129 <./atrop_example4.png>] [130 <./atrop_example5.png> <./atrop_representation2.png>] [131 <./query_bonds.png>] [132 <./query_bonds.2.png> <./query_atoms.png>] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 []\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1 /txtt/m/n/10 true \T1/qtm/m/n/10 non-tetrahedral chi-ral-ity will be per- Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/qtm/m/n/10 ceived from 3D co-or-di-nates. The de-fault value is \T1/txtt/m/ n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-ment vari- Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/qtm/m/n/10 able \T1/txtt/m/n/10 RDK_ENABLE_NONTETRAHEDRAL_STEREO \T1/qtm/m/ n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked from Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA llowNontetrahedralChirality() \T1/qtm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 12608--12618 \T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n /10 or from Python us-ing the func-tions Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 []\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per- Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is \T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION \T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked Underfull \hbox (badness 10000) in paragraph at lines 12620--12630 \T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality: :setUseLegacyStereoPerception() \T1/qtm/m/n/10 / [135] [136] Chapter 5. [137] [138 <./RDKitCB_0_im0.png> <./RDKitCB_0_im1.png>] [139 <./RDKitCB_0_im2.png> <./RDKitCB_40_im0.png>] [140 <./RDKitCB_40_im1.png> <./RDKitCB_23_im0.png>] [141 <./RDKitCB_23_im1.png> <./RDKitCB_32_im0.png>] [142 <./RDKitCB_32_im1.png> <./RDKitCB_1_im0.png (PNG copy)>] [143 <./RDKitCB_1_im1.png (PNG copy)> <./RDKitCB_1_im2.png (PNG copy)>] [144 <./RDKitCB_1_im3.png (PNG copy)> <./RDKitCB_2_im0.png>] [145 <./RDKitCB_2_im1.png> <./RDKitCB_36_im0.png>] [146 <./RDKitCB_36_im1.png>] [147 <./RDKitCB_38_im0.png>] [148 <./RDKitCB_39_im0.png (PNG copy)>] [149 <./RDKitCB_17_im0.png> <./RDKitCB_17_im1.png>] [150 <./RDKitCB_34_im0.png> <./RDKitCB_34_im1.png> <./RDKitCB_34_im2.png>] [151] Overfull \hbox (396.49246pt too wide) in paragraph at lines 13270--13270 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [152 <./RDKitCB_37_im0.png>] Overfull \hbox (396.49246pt too wide) in paragraph at lines 13299--13299 []\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C )C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C( =O)N(C)C(C(C)C)C(=O)N1C[][] [153 <./RDKitCB_37_im1.png>] [154 <./RDKitCB_37_im2.png>] [155 <./RDKitCB_35_im0.png>] [156] [157 <./RDKitCB_3_im0.png> <./RDKitCB_8_im0.png>] [158] [159 <./RDKitCB_30_im0.png>] [160 <./RDKitCB_30_im1.png>] [161 <./RDKitCB_7_im0.png> <./RDKitCB_7_im1.png>] [162 <./RDKitCB_7_im2.png (PNG copy)> <./RDKitCB_7_im3.png> <./RDKitCB_7_im4.pn g>] [163 <./RDKitCB_7_im5.png> <./RDKitCB_7_im6.png (PNG copy)>] [164] [165] [166 <./RDKitCB_29_im0.png (PNG copy)>] Underfull \vbox (badness 1043) detected at line 13953 [167 <./RDKitCB_33_im0.png (PNG copy)>] Overfull \vbox (0.99814pt too high) detected at line 13988 [168 <./RDKitCB_33_im1.png (PNG copy)>] [169 <./RDKitCB_33_im2.png (PNG copy)>] Overfull \hbox (490.99219pt too wide) in paragraph at lines 14054--14054 []\T1/txtt/m/n/10 "[][]CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C @H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@ @H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O[][] [170 <./RDKitCB_13_im0.png>] [171 <./RDKitCB_13_im1.png>] [172] [173 <./RDKitCB_20_im0.png>] [174 <./RDKitCB_21_im0.png>] [175 <./RDKitCB_21_im1.png>] [176 <./RDKitCB_21_im2.png (PNG copy)> <./RDKitCB_21_im3.png>] [177 <./RDKitCB_21_im4.png>] [178 <./RDKitCB_21_im5.png (PNG copy)>] [179 <./RDKitCB_22_im0.png>] [180 <./RDKitCB_22_im1.png>] [181 <./RDKitCB_6_im0.png (PNG copy)>] [182 <./RDKitCB_6_im1.png (PNG copy)> <./RDKitCB_6_im2.png (PNG copy)>] [183] [184] [185] [186] [187 <./RDKitCB_19_im0.png>] [188] [189] [190 <./RDKitCB_28_im0.png (PNG copy)> <./RDKitCB_28_im1.png (PNG copy)>] [191] [192] Chapter 6. [193] [194] [195] [196] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 15554--15554 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 15556--15556 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 15557--15557 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 15558--15558 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (464.74226pt too wide) in paragraph at lines 15559--15559 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC(=O)NC(C)(C)C(=O)NC( Cc1ccccc1)C(=O)NC(CC(C)C)C(=O)NC(Cc1ccccc1)C(=O)NC(CCCNC(=N)N)C(=O)N1CCCC1C(=O) NC(CCCNC(=N)N)C(=O)NC(CC(N)=O)C(N)=O| Overfull \hbox (359.74257pt too wide) in paragraph at lines 15560--15560 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 15561--15561 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 15562--15562 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 15563--15563 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \vbox (2.3893pt too high) detected at line 15565 [197] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 15577--15577 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H ]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](C)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H]2C SSC[C@H](NC1=O)C(=O)N[C@@H](Cc1cnc[nH]1)C(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CCCN C(=N)N)C(=O)N[C@@H](Cc1c[nH]c3ccccc13)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 15579--15579 []\T1/txtt/m/n/10 CN1C(=O)[C@H](CCCNC(=N)N)NC(=O)[C@@H](Cc2ccc(O)cc2)NC(=O)[C@@ H]2CCCN2C(=O)[C@H](Cc2ccc3ccccc3c2)NC(=O)[C@@H]1CC(=O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 15580--15580 []\T1/txtt/m/n/10 NCCCC[C@H](NC(=O)[C@H](Cc1ccc(OP(=O)(O)O)cc1)NC(=O)Cc1ccccc1) C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc1ccccc1)C(N)=O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 15581--15581 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC(=O)CN(CC(=O)NC(C)(C)C(=O)N[C@@H](Cc1ccccc1 )C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N1CCC[ C@H]1C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CC(N)=O)C(N)=O)C(=O)c1cccnc1| Overfull \hbox (359.74257pt too wide) in paragraph at lines 15582--15582 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CCSC)NC1=O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 15583--15583 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC( =O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O) [C@H](CC[S+](C)[O- Overfull \hbox (422.74239pt too wide) in paragraph at lines 15584--15584 []\T1/txtt/m/n/10 CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc 2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCSC)NC(=O)[C@H](CC( C)C)NC(=O)[C@H](CC[S+](C)[O- Overfull \hbox (249.49289pt too wide) in paragraph at lines 15585--15585 []\T1/txtt/m/n/10 ])NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H] (Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CC[S+](C)[O- Overfull \hbox (522.4921pt too wide) in paragraph at lines 15586--15586 []\T1/txtt/m/n/10 CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@H] (C(=O)N1CCC[C@H]1C(=O)N1CCC[C@H]1C(=O)N[C@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CC(C )C)C(=O)O)Cc1ccccc1)Cc1ccccc1)C(C)C)[C@@H](C)CC| [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] Chapter 7. [213] [214] [215] Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 16807--16811 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [216] [217] [218] Chapter 8. [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] Chapter 9. [231] [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 18704--18708 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [234] [235] [236] [237] [238] Overfull \vbox (0.8796pt too high) detected at line 19141 [239] [240] Underfull \hbox (badness 6691) in paragraph at lines 19244--19246 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] Overfull \vbox (1.8739pt too high) detected at line 20261 [253] [254] [255] [256] Chapter 10. [257] [258] Chapter 11. (./RDKit.ind) [259] (./RDKit.aux) ) (see the transcript file for additional information) Output written on RDKit.pdf (269 pages, 2935735 bytes). Transcript written on RDKit.log. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Have index file 'RDKit.idx', RDKit.ind RDKit Latexmk: All targets (RDKit.pdf) are up-to-date make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex' pdflatex finished; the PDF files are in _build/latex. make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.2/Docs/Book' make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' cp -r rdkit obj-*/ find /build/reproducible-path/rdkit-202409.2 -name rdchem.so /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib:" dh_auto_test cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j20 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: testCoordGen 1: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen/testCoordGen 1: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen 1: Test timeout computed to be: 1500 test 2 Start 2: pyCoordGen 2: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/External/CoordGen/Wrap/testCoordGen.py" 2: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen/Wrap 2: Test timeout computed to be: 1500 test 3 Start 3: testDict 3: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral/testDict 3: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral 3: Test timeout computed to be: 1500 test 4 Start 4: testRDValue 4: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral/testRDValue 4: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral 4: Test timeout computed to be: 1500 test 5 Start 5: testConcurrentQueue 5: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral/testConcurrentQueue 5: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral 5: Test timeout computed to be: 1500 test 6 Start 6: dictTestsCatch 6: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral/dictTestsCatch 6: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral 6: Test timeout computed to be: 1500 test 7 Start 7: logTestsCatch 7: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral/logTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral 7: Test timeout computed to be: 1500 test 8 Start 8: testDataStructs 8: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/testDataStructs 8: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs 8: Test timeout computed to be: 1500 test 9 Start 9: testFPB 9: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/testFPB 9: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs 9: Test timeout computed to be: 1500 test 10 Start 10: testMultiFPB 10: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/testMultiFPB 10: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs 10: Test timeout computed to be: 1500 test 11 Start 11: catchDataStructs 11: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/catchDataStructs 11: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs 11: Test timeout computed to be: 1500 test 12 Start 12: pyBV 12: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testBV.py" 12: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 test 13 Start 13: pyDiscreteValueVect 13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testDiscreteValueVect.py" 13: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 13: Test timeout computed to be: 1500 test 14 Start 14: pySparseIntVect 14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testSparseIntVect.py" 14: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 test 15 Start 15: pyFPB 15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testFPB.py" 15: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs/Wrap 15: Test timeout computed to be: 1500 test 16 Start 16: testTransforms 16: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/testTransforms 16: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry 16: Test timeout computed to be: 1500 test 17 Start 17: testGrid 17: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/testGrid 17: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry 17: Test timeout computed to be: 1500 test 18 Start 18: geometryTestsCatch 18: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/geometryTestsCatch 18: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry 18: Test timeout computed to be: 1500 test 19 Start 19: testPyGeometry 19: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap/testGeometry.py" 19: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/Wrap 19: Test timeout computed to be: 1500 test 20 Start 20: testMatrices 20: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/testMatrices 20: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics 20: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: 1: 4 4 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6496 0.9080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3926 -0.0584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4726 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3396 -0.0616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2048 -0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.3590 -0.3156 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.6160 0.6508 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: 0.2846 -0.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2790 -1.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5898 -2.2466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4530 -1.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4476 -0.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5788 -0.2468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5732 0.7532 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2956 1.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3012 2.2482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1700 2.7434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1590 0.7434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1534 -0.2564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: 1.7868 0.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6532 1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5187 0.7785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5180 -0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6515 -0.7209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7860 -0.2201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9195 -0.7195 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0539 -0.2189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8124 -0.7181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.6780 -0.2175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5445 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4101 -0.2161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.2764 -0.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1421 -0.2147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0547 0.7811 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9211 1.2805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 9 10 0 0 0 0 0 0 0 0999 V2000 1: 0.6718 -0.9994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5374 -0.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5366 0.5012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6702 1.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1954 0.4998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1946 -0.5002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1454 -0.8098 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7338 -0.0014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1466 0.8082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 1 1 0 1: 9 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: -0.5657 -0.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4321 -0.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2977 -0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2969 -1.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1625 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4329 0.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5673 1.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5681 2.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2975 2.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2975 2.5728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7969 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2991 0.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2999 -0.4278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2513 -0.7362 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5609 -1.6870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5393 -1.8942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8923 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8381 0.0734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2499 0.8820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: 0.5360 -0.9365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -1.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4020 -2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 1.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 2.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8300 3.4295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 -0.7457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.5900 -1.6966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9208 -2.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5682 -1.9046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8686 0.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 0.8725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 5 4 0 0 0 0 0 0 0 0999 V2000 1: 1.2134 -0.4976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3444 1.0006 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5186 -0.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3856 -0.0028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: -1.7333 -0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8661 -0.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8641 0.9303 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0011 -0.5713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8659 -0.0731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8679 0.9269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7309 -0.5749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 5 7 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: 1.2227 -0.4921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3350 1.0058 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5185 -0.5117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3902 -0.0216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2506 -0.5314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4014 0.9784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 5 7 1 0 1: M END 1: 1: test1 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: -0.2902 0.4155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5740 0.9187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4418 0.4219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3060 0.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3024 1.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4454 -0.5781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5812 -1.0813 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2866 -0.5843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1508 -1.0875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0186 -0.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0222 0.4095 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8828 -1.0937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 2 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 3 6 2 0 1: 6 7 1 0 1: 7 8 2 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 2 0 1: 10 12 1 0 1: 8 1 1 0 1: M END 1: 1: test2 1: RDKit 2D 1: 1: 5 4 0 0 0 0 0 0 0 0999 V2000 1: -0.4980 0.7210 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0004 -0.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8678 -0.6440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5020 0.7182 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8642 -0.6488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 1 0 1: 2 5 1 0 1: M END 1: 3: [09:08:12] Testing Github940: property dictionaries leaking memory 3: [09:08:12] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 4: min: 2.22507e-308 2.22507e-308 4: min: 1.17549e-38 1.17549e-38 4: min: 0 0 4: == int 4: == double 4: == float 4: == unsigned int 4: == bool 4: == std::string 5: [09:08:12] 5: ----------------------------------------- 5: [09:08:12] Finished: testPushAndPop() 5: [09:08:12] 5: ----------------------------------------- 5: [09:08:12] 5: ----------------------------------------- 6: Randomness seeded to: 2222902983 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: 7: [09:08:12] should not be silent 7: [09:08:12] should not be silent 7: Randomness seeded to: 128778159 7: [09:08:12] should not be silent 7: [09:08:12] should not be silent 7: [09:08:12] should not be silent 7: [09:08:12] should not be silent 7: [09:08:12] should not be silent 7: [09:08:12] should not be silent 7: [09:08:12] should not be silent 7: [09:08:12] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: 8: [09:08:12] pass 8: [09:08:12] v3 4 8: [09:08:12] v4 5 8: [09:08:12] SPARSE ----------------------------------- 8: [09:08:12] Set 10: 0 8: [09:08:12] Set 11: 0 8: [09:08:12] Set 14: 0 8: [09:08:12] Set 10: 1 8: [09:08:12] Get 14: 1 8: [09:08:12] Num: 20 8: [09:08:12] NumOn: 3 8: [09:08:12] NumOff: 17 8: 10, 11, 14, 8: [09:08:12] t2[19]: 0 8: [09:08:12] t2[14]: 1 8: [09:08:12] t2[19]: 0 8: [09:08:12] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, 8: t1&t2: 10, 11, 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 8: [09:08:12] Explicit ---------------------------------- 8: [09:08:12] Set 10: 0 8: [09:08:12] Set 11: 0 8: [09:08:12] Set 14: 0 8: [09:08:12] Set 10: 1 8: [09:08:12] Get 14: 1 8: [09:08:12] Num: 20 8: [09:08:12] NumOn: 3 8: [09:08:12] NumOff: 17 8: 10, 11, 14, 8: [09:08:12] t2[19]: 0 8: [09:08:12] t2[14]: 1 8: [09:08:12] t2[19]: 0 8: [09:08:12] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, 8: t1&t2: 10, 11, 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 8: [09:08:12] Done 8: [09:08:12] Test DiscreteValue Vectors 1 ---------------------------- 8: [09:08:12] Expected failure: Value out of range 8: [09:08:12] Expected failure: Value out of range 8: [09:08:12] Expected failure: Value out of range 8: [09:08:12] Expected failure: Value out of range 8: [09:08:12] Expected failure: Value out of range 8: [09:08:12] Test DiscreteValue Vectors 2 ------------------------------ 8: [09:08:12] Test DiscreteValue Vectors 3 --------------------------- 8: [09:08:12] Test DiscreteValue Operations ----------------------------- 8: [09:08:12] Test DiscreteValue Operations 2 -------------------------- 8: [09:08:12] Test SparseIntVect ------------------------------------ 8: [09:08:12] Test SparseIntVect Serialization -------------------------- 8: [09:08:12] Test BitVect Serialization ------------------------------- 8: [09:08:12] Test BitVect to FPS ------------------------------- 8: [09:08:12] Test BitVect to binary string ------------------------------- 8: [09:08:12] Test Similarity Measures BitVect ------------------------------- 8: [09:08:12] Test Similarity Measures SparseBitVect ------------------------------- 8: [09:08:12] Test BitVect with all ones ------------------------------- 8: [09:08:12] Test Explicit BitVects: Concatenation Operation ------------------------------- 8: [09:08:12] Test bitmap operations ------------------------------- 8: [09:08:12] Test bitmaps as properties ------------------------------- 8: [09:08:12] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- 11: Randomness seeded to: 2532056721 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: 16: **************************************** 16: testPointND 16: **************************************** 16: testPointOps3D 16: **************************************** 16: testPointOps2D 16: **************************************** 16: test12D 16: ref1: 1.0719 4.54672 ref2: 4.83545 4.43335 16: pt1: 2.16668 1.2005 pt2: 4.03205 3.84592 16: **************************************** 16: test23D 16: **************************************** 16: test3MatMultiply 16: Pt1: 1 0 0 Pt2: 2 0 0 16: -Pt1: -1 -0 -0 16: tp1: 0 0 0 tp2: 0 0 0 16: tp1: 0 0 0 tp2: 0 0 0 16: tp1: 0 0 3 tp2: 0 0 3 16: npt1: 0 0 3 npt2: 0 0 4 16: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 16: **************************************** 16: testFromQuaternion 16: **************************************** 20: [09:08:12] ----------------------------------------- 20: [09:08:12] Testing RDNumerics: vectors and matrices Code 20: [09:08:12] --------------------------------------- 20: [09:08:12] test1Vector 20: [09:08:12] --------------------------------------- 20: [09:08:12] test2Matrix 20: [09:08:12] --------------------------------------- 20: [09:08:12] test3SquareMatrix 20: [09:08:12] --------------------------------------- 20: [09:08:12] test4SymmMatrix 1/230 Test #4: testRDValue ............................ Passed 0.05 sec 2/230 Test #6: dictTestsCatch ......................... Passed 0.05 sec 3/230 Test #7: logTestsCatch .......................... Passed 0.05 sec 4/230 Test #8: testDataStructs ........................ Passed 0.04 sec 5/230 Test #9: testFPB ................................ Passed 0.04 sec 6/230 Test #10: testMultiFPB ........................... Passed 0.04 sec 7/230 Test #11: catchDataStructs ....................... Passed 0.04 sec 8/230 Test #16: testTransforms ......................... Passed 0.02 sec test 21 Start 21: testConrec 21: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/testConrec 21: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics 21: Test timeout computed to be: 1500 test 22 Start 22: testAlignment 22: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment 22: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment 22: Test timeout computed to be: 1500 test 23 Start 23: pyAlignment 23: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/Wrap/testAlignment.py" 23: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap 23: Test timeout computed to be: 1500 test 24 Start 24: testOptimizer 24: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer 24: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Optimizer 24: Test timeout computed to be: 1500 test 25 Start 25: ForceFieldsCatch 25: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/ForceFieldsCatch 25: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField 25: Test timeout computed to be: 1500 test 26 Start 26: testUFFForceField 26: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField 26: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/UFF 26: Test timeout computed to be: 1500 test 27 Start 27: testMMFFForceField 27: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField 27: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/MMFF 27: Test timeout computed to be: 1500 test 28 Start 28: pyForceFieldConstraints 28: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ForceField/Wrap/testConstraints.py" 28: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/Wrap 28: Test timeout computed to be: 1500 18: Randomness seeded to: 4075087753 18: =============================================================================== 18: All tests passed (50 assertions in 5 test cases) 18: 9/230 Test #18: geometryTestsCatch ..................... Passed 0.07 sec 17: *********************************************************** 17: Testing Grid 17: --------------------------------- 17: testUniformGrid1 17: 17: --------------------------------- 17: testUniformGrid2 17: 17: --------------------------------- 17: testUniformGridPickling 17: 17: --------------------------------- 17: testGridOps 17: 17: --------------------------------- 17: testUniformGridIndexing 17: 22: ----------------------------------------- 22: Testing Alignment Code 22: --------------------------------------- 22: testBasic 22: --------------------------------------- 22: testTriangle 22: --------------------------------------- 22: testFourPts 22: --------------------------------------- 22: testReflection 22: --------------------------------------- 24: ------------------------------------- 24: Testing linear search. 24: done 24: ------------------------------------- 24: Testing BFGS optimization. 24: done 26: ------------------------------------- 26: Unit tests for force field basics. 26: done 26: ------------------------------------- 26: Unit tests for basics of UFF bond-stretch terms. 26: done 26: ------------------------------------- 26: Unit tests for UFF bond-stretch terms. 26: done 26: ------------------------------------- 26: Unit tests for basics of UFF angle terms. 26: done 26: ------------------------------------- 26: Unit tests for UFF angle-bend terms. 26: theta = 3.14159; theta0 = 3.14159 26: theta = 2.094395, param1.theta0 = 2.094395 26: done 26: ------------------------------------- 26: Test Simple UFF molecule optimizations. 26: done 26: ------------------------------------- 26: Unit tests for UFF nonbonded terms. 26: done 26: ------------------------------------- 26: Test UFF torsional terms. 26: done 26: ------------------------------------- 26: Test UFF Parameter objects 26: ------------------------------------- 26: Test Simple UFF molecule optimization, part 2. 26: done 26: ------------------------------------- 26: Test UFF Torsion Conflicts. 26: C 0.4783 -0.7477 -0.0753 26: C -0.5465 -0.0176 0.3519 26: C -0.5114 1.4472 0.0870 26: H -1.5201 -0.4838 0.2485 26: H 0.4696 1.8363 0.3367 26: O -1.2618 1.9423 0.6934 26: F -0.7163 1.6298 -0.9622 26: done 26: ------------------------------------- 26: Unit tests for UFF distance constraint terms. 26: done 26: ------------------------------------- 26: Unit tests for all UFF constraint terms. 27: ------------------------------------- 27: Official MMFF validation suite. 10/230 Test #17: testGrid ............................... Passed 0.07 sec 11/230 Test #20: testMatrices ........................... Passed 0.06 sec 12/230 Test #22: testAlignment .......................... Passed 0.05 sec 13/230 Test #24: testOptimizer .......................... Passed 0.04 sec test 29 Start 29: testDistGeom 29: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom 29: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom 29: Test timeout computed to be: 1500 test 30 Start 30: pyDistGeom 30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap/rough_test.py" 30: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/Wrap 30: Test timeout computed to be: 1500 test 31 Start 31: graphmolTest1 31: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 31: Test timeout computed to be: 1500 test 32 Start 32: graphmolcpTest 32: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest 32: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 32: Test timeout computed to be: 1500 test 33 Start 33: graphmolqueryTest 33: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest 33: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 25: Randomness seeded to: 2277183330 25: =============================================================================== 25: All tests passed (20 assertions in 2 test cases) 25: 3: static boost any:0.115242 s 21: Randomness seeded to: 3525788632 21: =============================================================================== 21: All tests passed (76 assertions in 3 test cases) 21: 29: *********************************************************** 29: test1 29: *********************************************************** 29: testIssue216 29: Rows: 4 Columns: 4 29: 0 1 1 1 29: 1 0 1 1 29: 1 1 0 1 29: 1 1 1 0 29: *********************************************************** 29: 14/230 Test #21: testConrec ............................. Passed 0.12 sec 15/230 Test #25: ForceFieldsCatch ....................... Passed 0.10 sec 16/230 Test #29: testDistGeom ........................... Passed 0.07 sec test 34 Start 34: graphmolMolOpsTest 34: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest 34: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 test 35 Start 35: graphmoltestChirality 35: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality 35: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 test 36 Start 36: graphmoltestPickler 36: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler 36: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 32: 32: 32: 32: COPY 31: Atoms: 31: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 31: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 31: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 31: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 31: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 31: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 31: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 31: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: arom?: 1 query: AtomAtomicNum 31: 8 22 Ti chg: 0 deg: 1 exp: N/A imp: N/A hyb: 31: Bonds: 31: 0 0->1 order: 1 31: 1 1->2 order: 2 31: 2 2->3 order: 1 31: 3 0->4 order: 1 31: 4 5->6 order: 3 31: 5 6->7 order: 1 31: 6 7->8 order: 2 31: [09:08:12] 31: 31: **** 31: Pre-condition Violation 31: bond already exists 31: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp 31: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 31: 3# 0x00005631E6C5602C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:12] 31: 31: **** 31: Pre-condition Violation 31: bond already exists 31: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp 31: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 31: 3# 0x00005631E6C442F8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:12] 31: 31: **** 31: Pre-condition Violation 31: attempt to add self-bond 31: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp 31: Failed Expression: atomIdx1 != atomIdx2 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 31: 3# 0x00005631E6C444DE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:12] 31: 31: **** 31: Pre-condition Violation 31: bond already exists 31: Violation occurred on line 419 in file ./Code/GraphMol/ROMol.cpp 31: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 31: 3# 0x00005631E6C4451B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:12] 31: 31: **** 31: Pre-condition Violation 31: attempt to add self-bond 31: Violation occurred on line 417 in file ./Code/GraphMol/ROMol.cpp 31: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 31: 3# 0x00005631E6C4464E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:12] Explicit valence for atom # 0 B, 4, is greater than permitted 31: [09:08:12] Explicit valence for atom # 0 B, 4, is greater than permitted 31: [09:08:13] 31: 31: **** 31: Post-condition Violation 31: Element 'Xx' not found 31: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 31: Failed Expression: anum > -1 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 3# 0x00005631E6C78917 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00005631E6C614DD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 5# 0x00005631E6C50050 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 6# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 8# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:13] ------------------------------------- 31: [09:08:13] Test github381: thread-safe initialization of the periodic table 33: [09:08:13] ---------------------- Test1 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test2 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test3 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test4 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test5 33: [09:08:13] Done! 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test issue 2892580 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test github issue 53: query molecules not matching [R] 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test queries using qualifiers instead of == 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test Github issue 165: radicals not used in atom-atom matching 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test extra atom queries 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test extra bond queries 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test num heteroatom neighbor queries 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test atom type queries 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Test Github #2471: dummy atom queries are flagged as complex 33: [09:08:13] Done! 33: [09:08:13] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() 33: [09:08:13] Done! 26: done 26: ------------------------------------- 26: Unit tests for copying UFF ForceFields. 17/230 Test #32: graphmolcpTest ......................... Passed 0.08 sec test 37 Start 37: graphmoltestPicklerGlobalSetting 37: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 37: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 26: done 26: ------------------------------------- 26: Unit test for UFF butane scan. 18/230 Test #33: graphmolqueryTest ...................... Passed 0.07 sec test 38 Start 38: graphmolIterTest 38: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest 38: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 38: Test timeout computed to be: 1500 35: -------------------------- 35: -------------------------- 35: C/C=C/C(C)Cl 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing String Pickle Roundtrips. 1: cyclosporine a 1: RDKit 2D 1: 1: 85 85 0 0 0 0 0 0 0 0999 V2000 1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 3 2 1 1 1: 3 4 1 0 1: 4 5 2 0 1: 4 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 2 0 1: 8 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 2 0 1: 12 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 16 17 2 0 1: 16 18 1 0 1: 18 19 1 0 1: 19 20 1 0 1: 20 21 2 0 1: 20 22 1 0 1: 22 23 1 0 1: 23 24 1 0 1: 24 25 2 0 1: 24 26 1 0 1: 26 27 1 0 1: 27 28 1 0 1: 28 29 2 0 1: 28 30 1 0 1: 30 31 1 0 1: 31 32 1 0 1: 32 33 2 0 1: 32 34 1 0 1: 34 35 1 0 1: 35 36 1 0 1: 36 37 2 0 1: 36 38 1 0 1: 38 39 1 0 1: 39 40 1 0 1: 40 41 2 0 1: 40 42 1 0 1: 43 42 1 6 1: 43 44 1 0 1: 44 45 2 0 1: 44 46 1 0 1: 43 47 1 0 1: 47 48 1 0 1: 48 49 1 6 1: 48 50 1 0 1: 50 51 1 0 1: 51 52 2 0 1: 52 53 1 0 1: 47 54 1 1 1: 42 55 1 0 1: 39 56 1 6 1: 56 57 1 0 1: 56 58 1 0 1: 38 59 1 0 1: 35 60 1 6 1: 60 61 1 0 1: 61 62 1 0 1: 61 63 1 0 1: 34 64 1 0 1: 31 65 1 6 1: 65 66 1 0 1: 66 67 1 0 1: 66 68 1 0 1: 30 69 1 0 1: 27 70 1 6 1: 23 71 1 6 1: 19 72 1 6 1: 72 73 1 0 1: 73 74 1 0 1: 73 75 1 0 1: 18 76 1 0 1: 15 77 1 6 1: 77 78 1 0 1: 77 79 1 0 1: 11 80 1 6 1: 80 81 1 0 1: 81 82 1 0 1: 81 83 1 0 1: 10 84 1 0 1: 6 85 1 0 1: 46 3 1 0 1: M END 1: 1: single-double 1: RDKit 2D 1: 1: 17 16 0 0 0 0 0 0 0 0999 V2000 1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 2 3 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 2 3 1: 11 12 1 0 1: 12 13 2 3 1: 13 14 1 0 1: 14 15 2 3 1: 15 16 1 0 1: 16 17 1 0 1: M END 1: 37: [09:08:13] done 1: cis-trans 1: RDKit 2D 1: 1: 10 9 0 0 0 0 0 0 0 0999 V2000 1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 2 0 1: 3 4 1 0 1: 4 5 2 0 1: 5 6 1 0 1: 6 7 2 0 1: 7 8 1 0 1: 8 9 2 0 1: 9 10 1 0 1: M END 1: 1: admntn 1: RDKit 2D 1: 1: 10 12 0 0 0 0 0 0 0 0999 V2000 1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 10 1 0 1: 8 1 1 0 1: 9 4 1 0 1: 10 2 1 0 1: M END 1: 35: [09:08:13] Conflicting single bond directions around double bond at index 2. 35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. 35: [09:08:13] Conflicting single bond directions around double bond at index 4. 35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. 35: [09:08:13] Conflicting single bond directions around double bond at index 15. 35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. 35: [09:08:13] Conflicting single bond directions around double bond at index 2. 35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. 35: [09:08:13] Conflicting single bond directions around double bond at index 1. 35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. 34: 1 1 2 34: 1 1 1 34: 2 1 0.75 34: path: 2 19/230 Test #37: graphmoltestPicklerGlobalSetting ....... Passed 0.04 sec test 39 Start 39: hanoiTest 39: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest 39: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: 1: 42 44 0 0 0 0 0 0 0 0999 V2000 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 2 4 2 0 1: 4 5 1 0 1: 5 6 3 0 1: 6 7 1 0 1: 7 8 2 0 1: 8 9 1 0 1: 9 10 3 0 1: 10 11 1 0 1: 11 12 2 0 1: 12 13 1 0 1: 13 14 3 0 1: 14 15 1 0 1: 15 16 2 0 1: 16 17 1 0 1: 16 18 1 0 1: 12 19 1 0 1: 19 20 2 0 1: 20 21 1 0 1: 20 22 1 0 1: 19 23 1 0 1: 23 24 3 0 1: 24 25 1 0 1: 25 26 1 0 1: 26 27 2 0 1: 27 28 2 0 1: 26 29 1 0 1: 29 30 3 0 1: 8 31 1 0 1: 31 32 2 0 1: 32 33 1 0 1: 32 34 1 0 1: 31 35 1 0 1: 35 36 3 0 1: 36 37 1 0 1: 37 38 2 0 1: 37 39 1 0 1: 39 40 2 0 1: 40 41 1 0 1: 40 42 1 0 1: 39 4 1 0 1: 15 7 1 0 1: 30 11 1 0 1: M END 1: 34: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 34: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 35: -------------------------------------------------- 27: 27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 20/230 Test #35: graphmoltestChirality .................. Passed 0.09 sec test 40 Start 40: graphmolMemTest1 40: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 40: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 31: [09:08:13] done 31: [09:08:13] ------------------------------------- 31: [09:08:13] Test github1041: Segfault for atom with no owner (expect some warnings) 31: [09:08:13] 31: 31: **** 31: Pre-condition Violation 31: no owner 31: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 31: Failed Expression: dp_mol 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# 0x00005631E6C6EB9B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 3# 0x00005631E6C5007D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 6# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:13] 31: 31: **** 31: Pre-condition Violation 31: no owner 31: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h 31: Failed Expression: dp_mol 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# 0x00005631E6C4F979 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 3# 0x00005631E6C5007D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 6# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:13] done 31: [09:08:13] ------------------------------------- 31: [09:08:13] Test github1041: Segfault for atom with no owner (expect some warnings) 31: [09:08:13] 31: 31: **** 31: Pre-condition Violation 31: no owner 31: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 31: Failed Expression: dp_mol 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# 0x00005631E6C6EB9B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 3# 0x00005631E6C50082 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 6# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:13] 31: 31: **** 31: Pre-condition Violation 31: no owner 31: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h 31: Failed Expression: dp_mol 31: ---------- 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# 0x00005631E6C4F979 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 3# 0x00005631E6C50082 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: 4# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 31: 6# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: 31: [09:08:13] done 31: [09:08:13] ------------------------------------- 31: [09:08:13] Test github1453: RWMol.clear() should reset the numBonds count. 31: [09:08:13] done 31: [09:08:13] ------------------------------------- 31: [09:08:13] Test range-based for loops. 31: [09:08:13] done 31: [09:08:13] ------------------------------------- 31: [09:08:13] Test github1642: Atom index type is too low for big molecules. 34: [09:08:13] Explicit valence for atom # 0 B, 5, is greater than permitted 21/230 Test #38: graphmolIterTest ....................... Passed 0.06 sec test 41 Start 41: resMolSupplierTest 41: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest 41: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 34: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted 34: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted 34: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted 34: [09:08:13] Explicit valence for atom # 1 Si, 7, is greater than permitted 39: [09:08:13] Testing the hanoi sort 39: [09:08:13] populating vectors 22/230 Test #1: testCoordGen ........................... Passed 0.33 sec 23/230 Test #40: graphmolMemTest1 ....................... Passed 0.03 sec test 42 Start 42: molBundleTest 42: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest 42: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 test 43 Start 43: testSGroup 43: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup 43: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing reading existing pickle file (v2). 14: ......... 14: ---------------------------------------------------------------------- 14: Ran 9 tests in 0.011s 14: 14: OK 23: ..... 23: ---------------------------------------------------------------------- 23: Ran 5 tests in 0.002s 23: 23: OK 23: Testing Alignment Wrapper code: 24/230 Test #42: molBundleTest .......................... Passed 0.07 sec test 44 Start 44: test-valgrind 44: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind 44: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 15: ......... 15: ---------------------------------------------------------------------- 15: Ran 9 tests in 0.052s 15: 15: OK 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing combining molecules using pickles. 36: Atoms: 36: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 36: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 36: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 36: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 36: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 36: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 36: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 36: Bonds: 36: 0 0->1 order: 1 36: 1 1->2 order: 1 36: 2 2->0 order: 1 36: 3 3->4 order: 1 36: 4 4->5 order: 1 36: 5 5->6 order: 1 36: 6 6->3 order: 1 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing Issue164: Roundtrip Pickle Failure. 2: .... 2: ---------------------------------------------------------------------- 2: Ran 4 tests in 0.041s 2: 2: OK 19: ........... 19: ---------------------------------------------------------------------- 19: Ran 11 tests in 0.056s 19: 19: OK 19: Testing Geometry wrapper 30: ...... 30: ---------------------------------------------------------------------- 30: Ran 6 tests in 0.001s 30: 30: OK 25/230 Test #43: testSGroup ............................. Passed 0.11 sec test 45 Start 45: graphmolTestsCatch 45: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 34: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing Issue219: Pickle Failure with Conformations. 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing Issue220: Pickle problems with bond stereochemistry. 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing query serialization. 36: [09:08:13] C=[$(C=O)] 36: [09:08:13] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing radical handling in pickles. 36: [09:08:13] done 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing sf.net issue 2788233. 26/230 Test #14: pySparseIntVect ........................ Passed 0.44 sec 27/230 Test #23: pyAlignment ............................ Passed 0.40 sec test 46 Start 46: graphmolOrganometallicsCatch 46: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch 46: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 test 47 Start 47: graphmolSGroupCatch 47: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch 47: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 47: Test timeout computed to be: 1500 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing sf.net issue 3202580. 36: mass! 13.0034 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing sf.net issue 3316407. 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing sf.net issue 3496759. 36: smi match: *C *C 36: smi match: **=* **=* 36: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O 36: smi match: *OS(=O)OC *OS(=O)OC 36: smi match: *S(=O)(=O)OC *S(=O)(=O)OC 36: smi match: O=COC=O O=COC=O 36: smi match: OO OO 36: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 36: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 36: smi match: nnnOC=O nnnOC=O 36: smi match: *=C=N *=C=N 36: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 36: smi match: SP(S)=S SP(S)=S 36: smi match: NP(N)(N)=O NP(N)(N)=O 36: smi match: cN=[N+]=[N-] cN=[N+]=[N-] 36: smi match: *CC=O *CC=O 36: smi match: NNC=O NNC=O 36: smi match: * * 36: smi match: C=P C=P 36: smi match: CC(=N)Cl CC(=N)Cl 36: smi match: N=O N=O 36: smi match: ** ** 36: smi match: N=C=N N=C=N 36: smi match: [C-]#[NH+] [C-]#[NH+] 36: smi match: O=CON(C=O)C=O O=CON(C=O)C=O 36: smi match: N#CC[OH] N#CC[OH] 36: smi match: N#CC=O N#CC=O 36: smi match: N#CS(=O)=O N#CS(=O)=O 36: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 36: smi match: N#CN=N N#CN=N 36: smi match: N=NCC=O N=NCC=O 36: smi match: CCCCCCC CCCCCCC 36: smi match: OCCOCCO OCCOCCO 36: smi match: SS SS 36: smi match: [SH] [SH] 36: smi match: *1CC1 *1CC1 36: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] 36: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] 36: smi match: NC(=S)N=N NC(=S)N=N 36: smi match: N#CS N#CS 36: smi match: cC[N+] cC[N+] 36: smi match: C*C=S C*C=S 36: smi match: N[CH2]C#N N[CH2]C#N 36: smi match: O=C1CCO1 O=C1CCO1 36: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] 36: smi match: O=C1CCN1 O=C1CCN1 36: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 36: smi match: C=CC=CC=CC=C C=CC=CC=CC=C 36: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 36: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 36: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 36: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 36: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 36: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 36: smi match: cN(=O)~O cN(=O)~O 36: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 36: smi match: N~NC=O N~NC=O 36: smi match: *=N~C *=N~C 36: smi match: CO*(=O)=O CO*(=O)=O 36: smi match: * * 36: smi match: * * 36: smi match: *C=C *C=C 36: smi match: N#CS N#CS 36: smi match: *C=S *C=S 36: smi match: *N *N 45: Randomness seeded to: 3206593127 45: [09:08:13] WARNING: not removing hydrogen atom without neighbors 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: [09:08:13] Explicit valence for atom # 1 N, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 N, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 N, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 N, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 2 O, 3, is greater than permitted 45: [09:08:13] Explicit valence for atom # 2 O, 3, is greater than permitted 45: [09:08:13] non-ring atom 2 marked aromatic 45: [09:08:13] non-ring atom 2 marked aromatic 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 1 2 3 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 1 2 3 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 45: [09:08:13] Explicit valence for atom # 1 O, 3, is greater than permitted 45: [09:08:13] Explicit valence for atom # 4 F, 2, is greater than permitted 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 28/230 Test #44: test-valgrind .......................... Passed 0.10 sec test 48 Start 48: graphmolAdjustQueryCatch 48: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch 48: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 36: smi match: *C(=C)C=O *C(=C)C=O 36: smi match: *C#C *C#C 36: smi match: N#CCO N#CCO 36: smi match: O=N(=O)CCO O=N(=O)CCO 36: smi match: N=CS N=CS 36: smi match: O=CNC(O)C=O O=CNC(O)C=O 36: smi match: C=C(C=O)C=O C=C(C=O)C=O 36: smi match: N=CC=O N=CC=O 36: smi match: *C(C=O)C=O *C(C=O)C=O 36: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 36: smi match: O=CC=CC=O O=CC=CC=O 36: smi match: O=CN(O)C=O O=CN(O)C=O 36: smi match: O=CN(S)C=O O=CN(S)C=O 36: smi match: O=CNC=O O=CNC=O 36: smi match: O=CNN=O O=CNN=O 36: smi match: O=CNNC=O O=CNNC=O 36: smi match: O=CNOC=O O=CNOC=O 36: smi match: O=CS O=CS 36: smi match: O=CSC=S O=CSC=S 36: smi match: S=CS S=CS 36: smi match: C=O C=O 36: smi match: *C=N *C=N 36: smi match: CCCCCCC CCCCCCC 36: smi match: CN=O CN=O 36: smi match: CS(=O)(=O)O CS(=O)(=O)O 36: smi match: O=C1CCO1 O=C1CCO1 36: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 36: smi match: C=CCO C=CCO 36: smi match: C=CC=N C=CC=N 36: smi match: C=CC=O C=CC=O 36: smi match: C=CC(=O)C=C C=CC(=O)C=C 36: smi match: C=CC=S C=CC=S 36: smi match: C=CC(=S)S C=CC(=S)S 45: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted 45: [09:08:13] WARNING: not removing hydrogen atom with dummy atom neighbors 45: [09:08:13] WARNING: not removing hydrogen atom with dummy atom neighbors 45: [09:08:13] WARNING: not removing hydrogen atom with wedged bond 45: [09:08:13] WARNING: not removing hydrogen atom without neighbors 45: [09:08:13] WARNING: not removing hydrogen atom without neighbors 45: [09:08:13] WARNING: not removing hydrogen atom without neighbors 45: [09:08:13] WARNING: not removing hydrogen atom without neighbors 45: [09:08:13] Unreasonable formal charge on atom # 0. 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: no atom 45: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: at 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x00005652782927D8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: no owner 45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 45: Failed Expression: dp_mol 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x0000565278292862 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: atom not associated with this molecule 45: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: &at->getOwningMol() == this 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x00005652782928F5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: no atom 45: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: at 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x00005652782929E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: no owner 45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 45: Failed Expression: dp_mol 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x0000565278292A71 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: atom not associated with this molecule 45: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: &at->getOwningMol() == this 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x0000565278292B0D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: no atom 45: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: at 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x0000565278293429 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: no owner 45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 45: Failed Expression: dp_mol 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x0000565278292C78 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: atom not associated with this molecule 45: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: &at->getOwningMol() == this 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x0000565278292D12 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: null atom passed in 45: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: atom_pin 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x0000565278293401 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: cannot take ownership of an atom which already has an owner 45: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x0000565278293028 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 34: [09:08:13] non-ring atom 0 marked aromatic 34: [09:08:13] non-ring atom 0 marked aromatic 34: [09:08:13] Conflicting single bond directions around double bond at index 17. 34: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. 34: starting ring finding 34: done 34: starting ring finding 34: done 34: starting ring finding 36: smi match: *C=C(*)C=C *C=C(*)C=C 36: smi match: C=CC=N C=CC=N 36: smi match: *N(*)C=C *N(*)C=C 36: smi match: C=CN(=O)=O C=CN(=O)=O 36: smi match: C=CN(O)=O C=CN(O)=O 36: smi match: C=CO C=CO 36: smi match: C=COC=O C=COC=O 36: smi match: C=CS C=CS 36: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 36: smi match: C=NCO C=NCO 36: smi match: C=NC=O C=NC=O 36: smi match: C=NN C=NN 36: smi match: C=NN=C C=NN=C 36: smi match: C=NO C=NO 36: smi match: C=NOC=O C=NOC=O 36: smi match: C=N=O C=N=O 36: smi match: N#CS N#CS 36: smi match: *CN=O *CN=O 36: smi match: NCN NCN 36: smi match: ON=CCN=O ON=CCN=O 36: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 36: smi match: N=C(N)S N=C(N)S 36: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 36: smi match: NC=S NC=S 36: smi match: NC(N)=S NC(N)=S 36: smi match: C=CN C=CN 36: smi match: NOC=O NOC=O 36: smi match: C1CN1 C1CN1 36: smi match: O=C1NNNN1 O=C1NNNN1 36: smi match: N=C(N)C(=N)N N=C(N)C(=N)N 36: smi match: N=C(N)O N=C(N)O 36: smi match: N=C(N)C(=N)S N=C(N)C(=N)S 36: smi match: *C=N *C=N 36: smi match: N=CC=O N=CC=O 36: smi match: N=CS N=CS 36: smi match: N=C=N N=C=N 36: smi match: N=C=O N=C=O 36: smi match: N=C=S N=C=S 36: smi match: NOC(=O)O NOC(=O)O 36: smi match: *C(O)=S *C(O)=S 36: smi match: C=CO C=CO 36: smi match: ON=CC=NO ON=CC=NO 36: smi match: *C[SH](=O)=O *C[SH](=O)=O 36: smi match: OS(=O)=O OS(=O)=O 36: smi match: N#CS N#CS 36: smi match: C=C(S)S C=C(S)S 36: smi match: N=C(N)S N=C(N)S 36: smi match: N=C(S)S N=C(S)S 36: smi match: NC(=S)S NC(=S)S 36: smi match: O=CNS O=CNS 36: smi match: S S 36: smi match: [SiH4] [SiH4] 36: smi match: NS NS 36: smi match: NCN NCN 36: smi match: cC(c)(O)O cC(c)(O)O 36: smi match: *C(c)O *C(c)O 36: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 36: smi match: cS(=O)(=O)O cS(=O)(=O)O 36: smi match: *c1ccccn1=O *c1ccccn1=O 36: smi match: *c1ccccn1 *c1ccccn1 36: smi match: *c1nccccn1 *c1nccccn1 36: smi match: C1COCOC1 C1COCOC1 36: smi match: C=S C=S 36: smi match: c=S c=S 36: smi match: S=CS S=CS 36: smi match: C=CN(=O)=O C=CN(=O)=O 36: smi match: C=CN(=O)O C=CN(=O)O 36: smi match: N=CC=O N=CC=O 36: smi match: C=CS C=CS 36: smi match: SC(S)(S)S SC(S)(S)S 36: smi match: OS(O)(O)O OS(O)(O)O 36: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O 36: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O 36: smi match: N#CS N#CS 36: smi match: C=NO C=NO 36: smi match: C=N[SH]=N C=N[SH]=N 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: cannot take ownership of an bond which already has an owner 45: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp 45: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x00005652782933DD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: [09:08:13] WARNING: not removing hydrogen atom without neighbors 45: [09:08:13] Explicit valence for atom # 1 F greater than permitted 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: plain atoms have no Query 45: Violation occurred on line 691 in file ./Code/GraphMol/Atom.cpp 45: Failed Expression: 0 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x000056527823BE4B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: plain atoms have no Query 45: Violation occurred on line 696 in file ./Code/GraphMol/Atom.cpp 45: Failed Expression: 0 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x000056527823BEE0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: plain bonds have no Query 45: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp 45: Failed Expression: 0 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x000056527823BB70 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] 45: 45: **** 45: Pre-condition Violation 45: plain bonds have no query 45: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp 45: Failed Expression: 0 45: ---------- 45: Stacktrace: 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 45: 3# 0x000056527823BC05 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 45: [09:08:13] Unusual charge on atom 0 number of radical electrons set to zero 45: [09:08:13] Unusual charge on atom 0 number of radical electrons set to zero 45: [09:08:13] Unusual charge on atom 0 number of radical electrons set to zero 45: [09:08:13] non-ring atom 0 marked aromatic 45: [09:08:13] non-ring atom 0 marked aromatic 45: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 9 C, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 3 N, 4, is greater than permitted 45: [09:08:13] Explicit valence for atom # 15 C, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 11 C, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 9 C, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 9 C, 5, is greater than permitted 45: [09:08:13] Explicit valence for atom # 9 C, 6, is greater than permitted 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 7 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 3 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 3 7 45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 3 7 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 29/230 Test #30: pyDistGeom ............................. Passed 0.45 sec test 49 Start 49: chiralityTestsCatch 49: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch 49: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 49: Test timeout computed to be: 1500 36: smi match: O=C(S)S O=C(S)S 36: smi match: N=C(S)S N=C(S)S 36: smi match: N=C(=N)S N=C(=N)S 36: smi match: O=N=O O=N=O 36: smi match: O=NO O=NO 36: smi match: ONO ONO 36: smi match: C1SCS1 C1SCS1 36: smi match: N=C=S N=C=S 36: smi match: N=C=N N=C=N 36: smi match: C1N=N1 C1N=N1 36: smi match: *CS *CS 36: smi match: SC(S)=C(S)S SC(S)=C(S)S 36: smi match: N=CC=NO N=CC=NO 36: smi match: N#CCC#N N#CCC#N 36: smi match: CON=O CON=O 36: smi match: C=CN C=CN 36: smi match: C=N[SH](=O)=O C=N[SH](=O)=O 36: smi match: NN=O NN=O 36: smi match: NC(=O)S NC(=O)S 36: smi match: N#CS N#CS 36: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 36: smi match: c=N c=N 36: smi match: C1COCO1 C1COCO1 36: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 36: smi match: O=CC=O O=CC=O 36: smi match: O=CNOC=O O=CNOC=O 36: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 36: smi match: ONO ONO 36: smi match: ON(~O)~O ON(~O)~O 36: smi match: OC1COC(O)C1 OC1COC(O)C1 36: smi match: OC1CCOC1O OC1CCOC1O 36: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 36: smi match: N=[N+]=N N=[N+]=N 36: smi match: N#CN N#CN 36: smi match: C=NN=C C=NN=C 36: smi match: *CCN(C)C *CCN(C)C 36: smi match: CNN CNN 36: smi match: *CC *CC 36: smi match: OCS OCS 36: smi match: C1NO1 C1NO1 36: smi match: COS(C)(=O)=O COS(C)(=O)=O 36: smi match: C1CO1 C1CO1 36: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 36: smi match: *C(*)=C *C(*)=C 36: smi match: N#[NH+] N#[NH+] 36: smi match: C#NO C#NO 36: smi match: OOO OOO 36: smi match: OO OO 36: smi match: O~Cl(~O)~O O~Cl(~O)~O 34: done 34: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C 34: starting sanitization 30/230 Test #19: testPyGeometry ......................... Passed 0.54 sec 3: dynamic boost any:0.387596 s 31/230 Test #15: pyFPB .................................. Passed 0.55 sec 32/230 Test #2: pyCoordGen ............................. Passed 0.59 sec 47: Randomness seeded to: 1111466049 47: =============================================================================== 47: All tests passed (136 assertions in 8 test cases) 47: test 50 Start 50: canonTestsCatch 50: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch 50: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 test 51 Start 51: moliteratorTestsCatch 51: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 test 52 Start 52: queryTestsCatch 52: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 36: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O 36: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 36: smi match: *N *N 36: smi match: *P *P 36: smi match: *S *S 36: smi match: *C(*)(*)C=C *C(*)(*)C=C 36: smi match: *C(*)(*)C=C *C(*)(*)C=C 36: smi match: *C(*)C=C *C(*)C=C 36: smi match: *CC=C *CC=C 36: smi match: CN=C=O CN=C=O 36: smi match: CN=C=S CN=C=S 36: smi match: *C=O *C=O 36: smi match: N=N N=N 36: smi match: SS SS 36: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 36: smi match: CSC(C)=N CSC(C)=N 36: smi match: COC(C)=N COC(C)=N 36: smi match: C=C=C C=C=C 36: smi match: *C(=O)OC=O *C(=O)OC=O 36: smi match: C=CC#N C=CC#N 36: smi match: C=CC=O C=CC=O 36: smi match: CC=CC(C)=O CC=CC(C)=O 36: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 36: smi match: C#CC#N C#CC#N 36: smi match: C#CC=O C#CC=O 36: smi match: C#CC(=O)OCC C#CC(=O)OCC 36: smi match: C#CC=O C#CC=O 36: smi match: *C(=O)C#C *C(=O)C#C 36: smi match: C=CC=O C=CC=O 36: smi match: *C(*)(*)O *C(*)(*)O 36: smi match: COS(O)(=O)=O COS(O)(=O)=O 36: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] 36: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 36: smi match: *C(*)(*)C=O *C(*)(*)C=O 36: smi match: *C(*)(*)C=O *C(*)(*)C=O 36: smi match: *C(*)C=O *C(*)C=O 36: smi match: *CC=O *CC=O 36: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 34: done 34: starting sanitization 34: done 34: starting ring finding 34: done 34: starting ring finding 34: done 34: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 46: Randomness seeded to: 2855683568 46: =============================================================================== 46: All tests passed (62 assertions in 6 test cases) 46: 33/230 Test #46: graphmolOrganometallicsCatch ........... Passed 0.13 sec 34/230 Test #47: graphmolSGroupCatch .................... Passed 0.12 sec test 53 Start 53: molbundleTestsCatch 53: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 test 54 Start 54: pickleTestsCatch 54: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch 54: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 54: Test timeout computed to be: 1500 36: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 36: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 36: smi match: *C[SH](=O)=O *C[SH](=O)=O 36: smi match: * * 36: smi match: *1CC1 *1CC1 36: smi match: O=COC=O O=COC=O 36: smi match: N=C=O N=C=O 36: smi match: N=C=S N=C=S 36: smi match: O~O O~O 36: smi match: N~[SiH4] N~[SiH4] 36: smi match: *P *P 36: smi match: C=N=N C=N=N 36: smi match: *N#[NH+] *N#[NH+] 36: smi match: *S* *S* 36: smi match: ** ** 36: smi match: *CC* *CC* 36: smi match: *O[SiH3] *O[SiH3] 36: smi match: *OS(*)~O *OS(*)~O 36: smi match: N~N~O N~N~O 36: smi match: *N(~O)(~O)~O *N(~O)(~O)~O 36: smi match: *[N+](=C)[O-] *[N+](=C)[O-] 36: smi match: * * 36: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 36: smi match: *OCC#N *OCC#N 36: smi match: **C=C **C=C 36: smi match: C=C[O-] C=C[O-] 36: smi match: C=CO C=CO 36: smi match: * * 36: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 36: smi match: O=COn1ccnc1 O=COn1ccnc1 36: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 36: smi match: CC(C)(C)S CC(C)(C)S 36: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C 36: smi match: [CH]=O [CH]=O 36: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 36: smi match: SS SS 36: smi match: [SH] [SH] 36: smi match: *C* *C* 36: smi match: * * 36: smi match: C[nH3+] C[nH3+] 36: smi match: cC(=N)[NH2] cC(=N)[NH2] 36: smi match: O=CN[OH] O=CN[OH] 36: smi match: NN NN 36: smi match: * * 36: smi match: *OP(=O)O* *OP(=O)O* 36: smi match: * * 36: smi match: * * 36: smi match: * * 36: smi match: *N=C(*)* *N=C(*)* 36: smi match: *C(*)(*)C=O *C(*)(*)C=O 36: smi match: CSC=O CSC=O 36: smi match: * * 36: smi match: O=CCl O=CCl 36: smi match: *** *** 36: smi match: *C=O *C=O 36: smi match: C[OH] C[OH] 36: smi match: C[OH] C[OH] 36: smi match: C[OH] C[OH] 36: smi match: C[OH] C[OH] 36: smi match: C[CH]=O C[CH]=O 36: smi match: *=* *=* 34: [09:08:13] WARNING: not removing hydrogen atom with dummy atom neighbors 34: ------------------------------- 34: [09:08:13] Explicit valence for atom # 0 N, 4, is greater than permitted 34: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 34: [09:08:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 34: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 34: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 34: [09:08:13] WARNING: not removing hydrogen atom with dummy atom neighbors 28: ...[09:08:13] Molecule does not have explicit Hs. Consider calling AddHs() 26: done 48: Randomness seeded to: 479871284 48: =============================================================================== 48: All tests passed (281 assertions in 10 test cases) 48: 45: [09:08:13] Explicit valence for atom # 1 O, 3, is greater than permitted 45: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 45: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 45: [09:08:13] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. 45: [09:08:13] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom 45: [09:08:13] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom 45: [09:08:13] non-ring atom 0 marked aromatic 45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 51: Randomness seeded to: 2454161652 51: =============================================================================== 51: All tests passed (14 assertions in 4 test cases) 51: 52: Randomness seeded to: 1320834805 52: =============================================================================== 52: All tests passed (10 assertions in 1 test case) 52: 49: Randomness seeded to: 1826701960 49: [09:08:13] unable to set wavy bonds for double bonds: 3 35/230 Test #26: testUFFForceField ...................... Passed 0.55 sec 36/230 Test #48: graphmolAdjustQueryCatch ............... Passed 0.13 sec 37/230 Test #51: moliteratorTestsCatch .................. Passed 0.05 sec test 55 Start 55: tableTestsCatch 55: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/tableTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 test 56 Start 56: molopsTestsCatch 56: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 test 57 Start 57: smiTest1 57: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 57: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 36: smi match: *C *C 36: smi match: C#C C#C 36: smi match: *[CH]C=C *[CH]C=C 36: smi match: cCC(=O)[OH] cCC(=O)[OH] 36: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 36: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] 36: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 36: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 36: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O 36: smi match: *N(*)C*=O *N(*)C*=O 36: smi match: O=*C[OH] O=*C[OH] 36: smi match: *=C*=O *=C*=O 36: smi match: *=CC#N *=CC#N 36: smi match: *C[OH] *C[OH] 36: smi match: ** ** 36: smi match: *C[OH] *C[OH] 36: smi match: *C(*)=O *C(*)=O 36: smi match: * * 36: smi match: *CC(=O)[OH] *CC(=O)[OH] 36: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 36: smi match: *c *c 36: smi match: CN(C)c CN(C)c 36: smi match: c c 36: smi match: *c *c 36: smi match: *c *c 36: smi match: **:*cF **:*cF 36: smi match: cB([OH])[OH] cB([OH])[OH] 36: smi match: N~N~N N~N~N 36: smi match: *N=N* *N=N* 36: smi match: *CC[OH] *CC[OH] 36: smi match: *CC[OH] *CC[OH] 36: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] 36: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 36: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 36: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] 36: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O 36: smi match: *OC(*)=O *OC(*)=O 36: smi match: *C(=O)[OH] *C(=O)[OH] 36: smi match: O=C[OH] O=C[OH] 36: smi match: *OC(=O)O* *OC(=O)O* 36: smi match: * * 36: smi match: *OC(=O)Cl *OC(=O)Cl 36: smi match: *C#N *C#N 36: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 36: smi match: SS SS 36: smi match: * * 45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 38/230 Test #52: queryTestsCatch ........................ Passed 0.08 sec 49: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 49: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 3: static RDAny:0.061578 s 53: Randomness seeded to: 3092085464 53: =============================================================================== 53: All tests passed (6 assertions in 1 test case) 53: 39/230 Test #53: molbundleTestsCatch .................... Passed 0.07 sec test 58 Start 58: smiTest2 58: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 58: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 test 59 Start 59: cxsmilesTest 59: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 59: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 36: smi match: *=* *=* 36: smi match: *=* *=* 36: smi match: *=* *=* 36: smi match: *=* *=* 36: smi match: C1CO1 C1CO1 36: smi match: *OC(*)=O *OC(*)=O 36: smi match: * * 36: smi match: *O*[OH] *O*[OH] 36: smi match: COC(C)(C)O COC(C)(C)O 36: smi match: *[OH] *[OH] 36: smi match: ** ** 36: smi match: C=N[NH2] C=N[NH2] 36: smi match: C=NC=O C=NC=O 36: smi match: * * 36: smi match: C#NC C#NC 36: smi match: CN=C=O CN=C=O 36: smi match: CN=C=S CN=C=S 36: smi match: *OC(*)(*)O* *OC(*)(*)O* 36: smi match: *C(*)=O *C(*)=O 36: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 36: smi match: *~*=O *~*=O 36: smi match: *~*=O *~*=O 36: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] 36: smi match: * * 36: smi match: *C#N *C#N 36: smi match: *N(=O)~O *N(=O)~O 36: smi match: N N 36: smi match: OC(=O)C(O)=O OC(=O)C(O)=O 36: smi match: C=NO C=NO 36: smi match: O~O O~O 36: smi match: c[OH] c[OH] 36: smi match: O=P(~[OH])~O O=P(~[OH])~O 36: smi match: CO~P(=O)~O CO~P(=O)~O 36: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O 36: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 36: smi match: O=P(~O)~O O=P(~O)~O 36: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O 36: smi match: C[NH2] C[NH2] 36: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 36: smi match: * * 36: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 36: smi match: CS(C)~O CS(C)~O 36: smi match: CS(C)(~O)~O CS(C)(~O)~O 36: smi match: CS(N)(~O)~O CS(N)(~O)~O 36: smi match: CS([OH])(~O)~O CS([OH])(~O)~O 36: smi match: COS(C)(~O)~O COS(C)(~O)~O 36: smi match: *S(C)(~O)~O *S(C)(~O)~O 36: smi match: CN(C)C CN(C)C 36: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 36: smi match: *C(*)=S *C(*)=S 36: smi match: *OC(*)=S *OC(*)=S 36: smi match: * * 36: smi match: C[SH] C[SH] 36: smi match: c[SH] c[SH] 36: smi match: NC(N)=S NC(N)=S 36: smi match: * * 36: smi match: ***** ***** 36: smi match: NC(N)=O NC(N)=O 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing sf.net issue 280. 45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 49: [09:08:13] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 49: [09:08:13] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 49: [09:08:13] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 49: =============================================================================== 49: All tests passed (2267 assertions in 79 test cases) 49: 54: Randomness seeded to: 3337174469 54: =============================================================================== 54: All tests passed (45 assertions in 4 test cases) 54: 55: Randomness seeded to: 3594176814 55: =============================================================================== 55: All tests passed (7 assertions in 2 test cases) 55: 13: ...... 13: ---------------------------------------------------------------------- 13: Ran 6 tests in 0.004s 13: 13: OK 58: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' 58: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 58: [09:08:13] SMILES Parse Error: syntax error while parsing: - 58: [09:08:13] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' 58: [09:08:13] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' 58: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' 58: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 58: [09:08:13] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' 58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' 58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' 58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' 58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' 58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' 58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' 58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' 40/230 Test #49: chiralityTestsCatch .................... Passed 0.12 sec 41/230 Test #54: pickleTestsCatch ....................... Passed 0.08 sec 42/230 Test #55: tableTestsCatch ........................ Passed 0.06 sec 43/230 Test #58: smiTest2 ............................... Passed 0.03 sec test 60 Start 60: smaTest1 60: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 60: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 test 61 Start 61: smiTestCatch 61: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 61: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 test 62 Start 62: nontetrahedralCatch 62: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 62: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 test 63 Start 63: v2smiTestCatch 63: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch 63: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 63: Test timeout computed to be: 1500 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing sf.net issue 285. 36: [09:08:13] done 36: [09:08:13] done 36: [09:08:13] done 36: [09:08:13] done 36: [09:08:13] done 36: [09:08:13] done 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing Github2441: Add RDProps interface to Conformers. 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing Issue2510: Pickle Confs as double. 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing Github #2465: Negative atom-map numbers cause depickling to fail. 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing loading pickled mols with conformers 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing conformer reading/writing options 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing property reading options 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing property reading options 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing boost::serialization integration 36: [09:08:13] done 36: [09:08:13] ------------------------------------- 36: [09:08:13] Testing github issue 6036 45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 56: Randomness seeded to: 2903450028 56: =============================================================================== 56: All tests passed (72 assertions in 4 test cases) 56: 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] WARNING: not removing hydrogen atom without neighbors 57: [09:08:13] Invalid chiral specification on atom 0 57: [09:08:13] Invalid chiral specification on atom 0 57: [09:08:13] Invalid chiral specification on atom 0 57: [09:08:13] Invalid chiral specification on atom 0 57: [09:08:13] Invalid chiral specification on atom 0 57: [09:08:13] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' 57: [09:08:13] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 44/230 Test #36: graphmoltestPickler .................... Passed 0.55 sec 45/230 Test #56: molopsTestsCatch ....................... Passed 0.12 sec test 64 Start 64: testDepictor 64: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor 64: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor 64: Test timeout computed to be: 1500 test 65 Start 65: depictorCatch 65: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch 65: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor 65: Test timeout computed to be: 1500 45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 45: [09:08:13] Explicit valence for atom # 0 Al, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 0 Al, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 Si, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 Si, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 0 P, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 0 P, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 0 P, 7, is greater than permitted 61: Randomness seeded to: 3639760926 61: [09:08:13] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 61: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 61: [09:08:13] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' 61: [09:08:13] SMARTS Parse Error: unclosed ring for input: 'C1C' 62: Randomness seeded to: 1691186716 62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 46/230 Test #13: pyDiscreteValueVect .................... Passed 0.78 sec test 66 Start 66: pyDepictor 66: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Wrap/testDepictor.py" 66: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap 66: Test timeout computed to be: 1500 45: [09:08:13] Explicit valence for atom # 0 P, 7, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 As, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 As, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 As, 7, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 As, 7, is greater than permitted 45: [09:08:13] Explicit valence for atom # 0 Sb, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 0 Sb, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 0 Sb, 7, is greater than permitted 45: [09:08:13] Explicit valence for atom # 0 Sb, 7, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 Bi, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 Bi, 6, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 Bi, 8, is greater than permitted 45: [09:08:13] Explicit valence for atom # 1 Bi, 8, is greater than permitted 45: =============================================================================== 45: All tests passed (4464 assertions in 106 test cases) 45: 61: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 61: [09:08:13] SMARTS Parse Error: syntax error while parsing: C)foo 61: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' 61: [09:08:13] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| 61: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 61: [09:08:13] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' 62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 63: Randomness seeded to: 14398752 63: =============================================================================== 63: All tests passed (14 assertions in 2 test cases) 63: 47/230 Test #45: graphmolTestsCatch ..................... Passed 0.37 sec 48/230 Test #63: v2smiTestCatch ......................... Passed 0.08 sec test 67 Start 67: testMrvToMol 67: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 67: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse 67: Test timeout computed to be: 1500 test 68 Start 68: fileParsersTest1 68: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 68: Test timeout computed to be: 1500 62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 61: [09:08:13] w block attempts to set wedging on bond 0 more than once. 61: [09:08:13] improperly formatted w block 61: [09:08:13] atom 3 is not associated with bond 1(1-2) in w block 62: [09:08:13] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 62: =============================================================================== 62: All tests passed (308 assertions in 9 test cases) 62: 39: [09:08:13] sorting (hanoi sort) vectors 49/230 Test #62: nontetrahedralCatch .................... Passed 0.16 sec test 69 Start 69: testAtropisomers 69: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers 69: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 69: [09:08:13] ---- Running with POSIX locale ----- 61: [09:08:13] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' 61: [09:08:13] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' 61: [09:08:13] SMARTS Parse Error: syntax error while parsing: C1C)foo 61: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' 61: [09:08:13] SMILES Parse Error: extra close parentheses while parsing: C1C)foo 61: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' 61: =============================================================================== 61: All tests passed (1570 assertions in 66 test cases) 61: 50/230 Test #61: smiTestCatch ........................... Passed 0.20 sec test 70 Start 70: testSquiggleDoubleBonds 70: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds 70: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 59: Randomness seeded to: 3537694454 59: Test 59: 59: ShortAtropisomerNoCoords.cxsmi 59: 59: Test 59: 59: ShortAtropisomer.cxsmi 59: 59: Test 59: 59: ShortAtropisomerArom.cxsmi 59: 59: Test 59: 59: AtropManyChirals.cxsmi 59: 59: Test 59: 59: AtropManyChiralsEnhanced.cxsmi 59: 59: Test 59: 59: AtropManyChiralsEnhanced2.cxsmi 59: 59: Test 59: 59: AtropManyChiralsEnhanced3.cxsmi 59: 59: Test 59: 59: AtropManyChiralsEnhanced4.cxsmi 59: 59: Test 59: 59: BMS-986142_3d_chiral.cxsmi 59: 59: Test 59: 59: BMS-986142_3d.cxsmi 59: 59: Test 59: 59: BMS-986142_atrop1.cxsmi 59: 59: Test 59: 59: BMS-986142_atrop2.cxsmi 59: 59: Test 59: 59: BMS-986142_atrop3.cxsmi 59: 59: Test 59: 59: BMS-986142_atrop4.cxsmi 59: 59: Test 59: 59: BMS-986142_atrop5.cxsmi 59: 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: *************************************** 68: *************************************** 68: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 28: ......[09:08:13] Molecule does not have explicit Hs. Consider calling AddHs() 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 28: [09:08:13] 28: 28: **** 59: Test 59: 59: BMS-986142_atrop6.cxsmi 59: 59: Test 59: 59: BMS-986142_atropBad1.cxsmi 59: 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 28: Invariant Violation 28: bad direction in linearSearch 28: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h 28: Failed Expression: status >= 0 28: ---------- 28: Stacktrace: 28: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 28: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 28: 2# ForceFields::ForceField::minimize(unsigned int, std::vector >*, unsigned int, double, double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitForceField.so.1 28: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/ForceField/rdForceField.so 28: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 28: 5# 0x00007FED16AB362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 28: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 28: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 28: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 28: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 28: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 28: 11# 0x00007FED13FAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 28: 12# 0x00007FED13FAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 28: 13# 0x00007FED13FAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 28: 14# 0x00007FED13FAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 28: 15# 0x00007FED13FAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 28: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 28: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 28: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 28: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 28: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 28: 21# 0x00007FED16AB03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 28: 22# _PyObject_MakeTpCall in /usr/bin/python3 28: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 24# 0x0000000000546E76 in /usr/bin/python3 28: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 26# _PyObject_Call_Prepend in /usr/bin/python3 28: 27# 0x000000000059810D in /usr/bin/python3 28: 28# 0x0000000000593E22 in /usr/bin/python3 28: 29# _PyObject_MakeTpCall in /usr/bin/python3 28: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 31# 0x0000000000546E76 in /usr/bin/python3 28: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 33# _PyObject_Call_Prepend in /usr/bin/python3 28: 34# 0x000000000059D6E4 in /usr/bin/python3 28: 35# _PyObject_MakeTpCall in /usr/bin/python3 28: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 37# 0x0000000000546E76 in /usr/bin/python3 28: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 39# _PyObject_Call_Prepend in /usr/bin/python3 28: 40# 0x000000000059D6E4 in /usr/bin/python3 28: 41# _PyObject_MakeTpCall in /usr/bin/python3 28: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 43# 0x0000000000546E76 in /usr/bin/python3 28: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 45# _PyObject_Call_Prepend in /usr/bin/python3 28: 46# 0x000000000059D6E4 in /usr/bin/python3 28: 47# _PyObject_MakeTpCall in /usr/bin/python3 28: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 49# _PyObject_Call_Prepend in /usr/bin/python3 28: 50# 0x000000000059810D in /usr/bin/python3 28: 51# 0x0000000000593E22 in /usr/bin/python3 28: 52# _PyObject_MakeTpCall in /usr/bin/python3 28: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 28: 54# PyEval_EvalCode in /usr/bin/python3 28: 55# 0x00000000005FFE7F in /usr/bin/python3 28: 56# 0x00000000006A59F2 in /usr/bin/python3 28: 57# _PyRun_SimpleFileObject in /usr/bin/python3 28: 58# _PyRun_AnyFileObject in /usr/bin/python3 28: 59# Py_RunMain in /usr/bin/python3 28: 60# Py_BytesMain in /usr/bin/python3 28: 61# 0x00007FED17269D68 in /lib/x86_64-linux-gnu/libc.so.6 28: 62# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 28: 63# _start in /usr/bin/python3 28: ---------- 28: **** 28: 60: [09:08:13] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC 60: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' 60: [09:08:13] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON 60: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' 68: [09:08:13] bond with order 0 found on line 7. This is not part of the MDL specification. 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 59: Test 59: 59: BMS-986142_atropBad2.cxsmi 59: 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 57: --C1CCC2(CC1)CCCCC2CCC1CCCC1 60: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 60: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 51/230 Test #60: smaTest1 ............................... Passed 0.28 sec test 71 Start 71: testMolSupplier 71: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 71: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 68: [09:08:13] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 68: [09:08:13] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 68: [09:08:13] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 70: Randomness seeded to: 2214421694 70: =============================================================================== 70: All tests passed (15 assertions in 3 test cases) 70: 57: smi: ClC1CCCCC1 57: smi: ClC1CCCCC1 57: smi: ClC1CCCCC1Br 57: smi: c1ccccc1 57: smi: c1ccncc1 57: smi: c1cc[nH]c1 57: smi: c1cc[nH]c1 57: smi: c1cc[pH]c1 71: [09:08:13] 71: ----------------------------------------- 68: generating smiles 52/230 Test #70: testSquiggleDoubleBonds ................ Passed 0.09 sec test 72 Start 72: testGeneralFileReader 72: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 72: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 72: Test timeout computed to be: 1500 57: CbC(aC)aC 57: CaC(bC)aC 57: CbC(bC)aC 57: O.C 57: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 68: converting back 67: Using new chirality perception 67: Test 67: 67: rxnStereoMarkedCrossed.mrv 67: 67: Test 67: 67: NewChiralTest.sdf 67: 67: Test 67: 67: NewChiralTest.sdf 67: 67: Test 67: 67: NewChiralTestNoChiral.sdf 67: 67: Test 67: 67: NewChiralTestNoChiral.sdf 67: 67: Test 67: 67: NewChiralTestAllChiral.sdf 67: 67: Test 67: 67: NewChiralTestAllChiral.sdf 67: 67: Test 67: 67: vendor839.sdf 67: 67: Test 67: 67: ProblemShort.mol 67: 67: [09:08:13] For a MultipleSgroup expansion, the matching orphaned bond was not found 67: The multiple sgroup will be ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 65: Randomness seeded to: 2688638864 65: =============================================================================== 65: All tests passed (577 assertions in 17 test cases) 65: 57: [09:08:13] SMILES Parse Error: syntax error while parsing: c%()ccccc%() 57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' 57: [09:08:13] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) 57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' 57: [09:08:13] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' 57: [09:08:13] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' 68: check isomorphism 53/230 Test #65: depictorCatch .......................... Passed 0.25 sec test 73 Start 73: testMultithreadedMolSupplier 73: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 73: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 73: Test timeout computed to be: 1500 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 57: [09:08:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 57: [09:08:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 57: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 57: [09:08:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 57: [09:08:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 57: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 57: [09:08:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 57: [09:08:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 57: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 57: C=c1s/c2n(c1=O)CCCCCCC\N=2 71: [09:08:13] 71: 71: **** 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 71: Invariant Violation 71: bad prop value 71: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 71: Failed Expression: nSwaps < 2 71: ---------- 71: Stacktrace: 71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 71: 2# 0x00007F1A56F94AA4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 71: 4# 0x0000562969B8B3B4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 71: 5# 0x0000562969B60ADA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 71: 6# 0x0000562969B63E0B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 71: 7# 0x00007F1A56431D68 in /lib/x86_64-linux-gnu/libc.so.6 71: 8# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 71: 9# 0x0000562969B659D1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 71: ---------- 71: **** 71: 72: [09:08:13] 72: ----------------------------------------- 72: [09:08:13] Finished: testDetermineFormat() 72: [09:08:13] ----------------------------------------- 72: 72: [09:08:13] 72: ----------------------------------------- 57: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 57: [09:08:13] SMILES Parse Error: extra close parentheses while parsing: C) 57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 54/230 Test #57: smiTest1 ............................... Passed 0.40 sec test 74 Start 74: testMolWriter 74: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 74: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 74: Test timeout computed to be: 1500 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 59: Test 59: 59: JDQ443_3d.cxsmi 59: 59: Test 59: 59: JDQ443_atrop1.cxsmi 59: 59: Test 59: 59: JDQ443_atrop2.cxsmi 59: 59: Test 59: 59: JDQ443_atrop3.cxsmi 59: 59: Test 59: 59: JDQ443_atrop4.cxsmi 59: 59: Test 59: 59: JDQ443_atropBad1.cxsmi 59: 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 73: [09:08:13] 73: ----------------------------------------- 34: [09:08:13] Maximum BFS search size exceeded. 34: This is likely due to a highly symmetric fused ring system. 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 59: Test 59: 59: RP-6306_atrop1.cxsmi 59: 59: Test 59: 59: RP-6306_atrop2.cxsmi 59: 59: Test 59: 59: RP-6306_atrop3.cxsmi 59: 59: Test 59: 59: RP-6306_atrop4.cxsmi 59: 59: Test 59: 59: RP-6306_atrop5.cxsmi 59: 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 59: Test 59: 59: RP-6306_atrop6.cxsmi 59: 59: Test 59: 59: RP-6306_atropBad1.cxsmi 59: 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 59: Test 59: 59: RP-6306_atropBad2.cxsmi 59: 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 72: [09:08:13] Finished: testSdf() 72: [09:08:13] ----------------------------------------- 72: 72: [09:08:13] 72: ----------------------------------------- 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 28: ... 28: ---------------------------------------------------------------------- 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 3: dynamic RDAny:0.437495 s 3: static RDValue:1e-06 s 72: [09:08:13] Finished: testSmi() 72: [09:08:13] ----------------------------------------- 72: 72: [09:08:13] 72: ----------------------------------------- 28: Ran 12 tests in 0.650s 28: 28: OK 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [09:08:13] Warning: stereochemistry around double bond may be incorrect in depiction. 59: Test 59: 59: RP-6306_3d.cxsmi 59: 59: Test 59: 59: Sotorasib_atrop1.cxsmi 59: 59: Test 59: 59: Sotorasib_atrop2.cxsmi 59: 59: Test 59: 59: Sotorasib_atrop3.cxsmi 59: 59: Test 59: 59: Sotorasib_atrop4.cxsmi 59: 59: Test 59: 59: Sotorasib_atrop5.cxsmi 59: 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: Test 59: 59: Sotorasib_atropBad1.cxsmi 59: 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 59: Test 59: 59: Sotorasib_atropBad2.cxsmi 59: 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 59: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 59: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 59: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 71: [09:08:14] Finished: testMolSup() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testRandMolSup() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 69: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 59: Test 59: 59: Sotorasib_3d.cxsmi 59: 59: Test 59: 59: ZM374979_atrop1.cxsmi 59: 59: Test 59: 59: ZM374979_atrop2.cxsmi 59: 59: Test 59: 59: ZM374979_atrop3.cxsmi 59: 59: Test 59: 59: ZM374979_atrop4.cxsmi 59: 59: Test 59: 59: ZM374979_atropBad1.cxsmi 59: 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 71: [09:08:14] Finished: testSmilesSup() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] ------------------------------------------------------ 71: [09:08:14] SMILES Parse Error: syntax error while parsing: fail 71: [09:08:14] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 71: [09:08:14] ERROR: Smiles parse error on line 3 71: [09:08:14] ERROR: Cannot create molecule from : 'fail' 71: [09:08:14] ------------------------------------------------------ 71: [09:08:14] ------------------------------------------------------ 71: [09:08:14] >>> This may result in an infinite loop. It should finish almost immediately: 71: [09:08:14] <<< done. 71: [09:08:14] Finished: testSmilesSupFromText() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testSmilesWriter() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 55/230 Test #64: testDepictor ........................... Passed 0.53 sec test 75 Start 75: testTplParser 75: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 75: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 71: [09:08:14] Finished: testSDWriter() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testSDSupplierEnding() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testSuppliersEmptyFile() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testCisTrans() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testStereoRound() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71: [09:08:14] Finished: testIssue226() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testTDTSupplier1() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testTDTSupplier2() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 59: Test 59: 59: Mrtx1719_3d.cxsmi 59: 59: Test 59: 59: Mrtx1719_atrop1.cxsmi 59: 59: Test 59: 59: Mrtx1719_atrop2.cxsmi 59: 59: Test 59: 59: Mrtx1719_atrop3.cxsmi 59: 59: Test 59: 59: Mrtx1719_atrop4.cxsmi 59: 59: Test 59: 59: Mrtx1719_atropBad1.cxsmi 59: 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 72: [09:08:14] Finished: testMae() 72: [09:08:14] ----------------------------------------- 72: 72: [09:08:14] 72: ----------------------------------------- 71: [09:08:14] Finished: testTDTSupplier3() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testSDSupplierFromText() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] ERROR: Problems encountered parsing data fields 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] ERROR: Problems encountered parsing data fields 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Spurious data before the first property will be ignored 71: [09:08:14] Property will be truncated after the first blank line 71: [09:08:14] Property will be truncated after the first blank line 71: [09:08:14] Property will be truncated after the first blank line 71: [09:08:14] Finished: testSDSupplierStrLax1() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] ERROR: Problems encountered parsing data fields 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Property will be truncated after the first blank line 71: [09:08:14] Finished: testSDSupplierStrLax2() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] ERROR: Problems encountered parsing data fields 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] ERROR: Problems encountered parsing data fields 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Spurious data before the first property will be ignored 71: [09:08:14] Property will be truncated after the first blank line 71: [09:08:14] Property will be truncated after the first blank line 71: [09:08:14] Property will be truncated after the first blank line 71: [09:08:14] Finished: testSDSupplierFromTextStrLax1() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] ERROR: Problems encountered parsing data fields 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Property will be truncated after the first blank line 71: [09:08:14] Finished: testSDSupplierFromTextStrLax2() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testIssue265() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] ERROR: End of data field name not found 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Explicit valence for atom # 0 F, 2, is greater than permitted 71: [09:08:14] ERROR: Could not sanitize molecule ending on line 16 71: [09:08:14] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted 71: [09:08:14] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] ERROR: Bond line too short: 'M END' on line 18 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Finished: testSDErrorHandling() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 72: [09:08:14] Finished: testTdt() 72: [09:08:14] ----------------------------------------- 72: 71: [09:08:14] Finished: testIssue381() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 3: dynamic RDValue:0.080217 s 3: deleted! 3: [09:08:14] ------------------------------------- 3: [09:08:14] Testing String Pickle Roundtrips. 3: [09:08:14] done 3: [09:08:14] ------------------------------------- 3: [09:08:14] Testing conversion of vect to string. 3: [09:08:14] done 3: [09:08:14] ------------------------------------- 3: [09:08:14] Testing returning const references. 3: [09:08:14] any cast 3: [09:08:14] done: 0.001689 300000 3: [09:08:14] copy 71: [09:08:14] Finished: testSetStreamIndices() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testMixIterAndRandom() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: build: 71: [09:08:14] Finished: testRemoveHs() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 3: [09:08:14] done: 0.001596 300000 3: [09:08:14] ref 3: [09:08:14] done: 0.001619 300000 3: [09:08:14] dict 56/230 Test #72: testGeneralFileReader .................. Passed 0.34 sec test 76 Start 76: testMol2ToMol 76: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 76: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 76: Test timeout computed to be: 1500 3: [09:08:14] done: 0.004615 300000 3: [09:08:14] ref with hasVal 3: [09:08:14] done: 0.002449 300000 3: [09:08:14] done 3: [09:08:14] ------------------------------------- 3: [09:08:14] Testing dict update. 3: [09:08:14] done 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 71: [09:08:14] Finished: testGetItemText() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 57/230 Test #28: pyForceFieldConstraints ................ Passed 1.25 sec test 77 Start 77: testSequence 77: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence 77: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 58/230 Test #3: testDict ............................... Passed 1.36 sec test 78 Start 78: testExtendedStereoParsing 78: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 78: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 78: Test timeout computed to be: 1500 59/230 Test #75: testTplParser .......................... Passed 0.09 sec test 79 Start 79: fileParsersCatchTest 79: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 79: Test timeout computed to be: 1500 71: [09:08:14] Finished: testForwardSDSupplier() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testMissingCRSDSupplier() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testIssue3482695() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] ERROR: Cannot convert 'foo' to unsigned int on line 557 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Finished: testIssue3525673() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testBlankLinesInProps() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testSkipLines() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testGitHub23() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testGitHub88() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 60/230 Test #78: testExtendedStereoParsing .............. Passed 0.03 sec test 80 Start 80: testPropertyLists 80: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 80: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 80: Test timeout computed to be: 1500 71: [09:08:14] Finished: testGitHub2285() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 71: [09:08:14] ERROR: Smiles parse error on line 1 71: [09:08:14] ERROR: Cannot create molecule from : 'c1ccccc' 71: [09:08:14] SMILES Parse Error: extra open parentheses for input: 'C(C' 71: [09:08:14] ERROR: Smiles parse error on line 3 71: [09:08:14] ERROR: Cannot create molecule from : 'C(C' 71: [09:08:14] Explicit valence for atom # 1 C, 5, is greater than permitted 71: [09:08:14] ERROR: Could not sanitize molecule on line 5 71: [09:08:14] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 71: [09:08:14] Explicit valence for atom # 1 F, 2, is greater than permitted 71: [09:08:14] ERROR: Could not sanitize molecule ending on line 21 71: [09:08:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 71: [09:08:14] Explicit valence for atom # 1 F, 2, is greater than permitted 71: [09:08:14] ERROR: Could not sanitize molecule ending on line 21 71: [09:08:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 71: [09:08:14] Explicit valence for atom # 1 F, 2, is greater than permitted 71: [09:08:14] ERROR: Could not sanitize molecule ending on line 21 71: [09:08:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 71: [09:08:14] ERROR: Atom line too short: ' -9.6' on line 28 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Explicit valence for atom # 1 F, 2, is greater than permitted 71: [09:08:14] ERROR: Could not sanitize molecule ending on line 21 71: [09:08:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 71: [09:08:14] ERROR: Atom line too short: ' -9.6' on line 28 71: [09:08:14] ERROR: moving to the beginning of the next molecule 71: [09:08:14] Finished: testGitHub2479() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] 71: 71: **** 71: Invariant Violation 71: bad chiral bond 71: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 71: Failed Expression: bnd 71: ---------- 71: Stacktrace: 71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 71: 2# 0x00007F1A56F950BA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 71: 4# 0x0000562969B668CE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 71: 5# 0x0000562969B6575B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 71: 6# 0x00007F1A56431D68 in /lib/x86_64-linux-gnu/libc.so.6 71: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 71: 8# 0x0000562969B659D1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 71: ---------- 71: **** 71: 71: [09:08:14] Finished: testGitHub2881() 71: [09:08:14] ----------------------------------------- 71: 71: [09:08:14] ----------------------------------------- 71: [09:08:14] Finished: testGitHub3517() 71: [09:08:14] ----------------------------------------- 71: 69: Atropisomers- 1 hits 3 misses 69: Final results: 69: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses 61/230 Test #76: testMol2ToMol .......................... Passed 0.07 sec test 81 Start 81: XYZFileParserCatchTest 81: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 81: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 81: Test timeout computed to be: 1500 77: Sequence: GREG 77: HELM: PEPTIDE1{G.R.E.G}$$$$ 77: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 77: PDB: 77: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 77: CONECT 1 2 77: CONECT 2 3 77: CONECT 3 4 4 5 77: CONECT 5 6 77: CONECT 6 7 9 77: CONECT 7 8 8 16 77: CONECT 9 10 77: CONECT 10 11 77: CONECT 11 12 77: CONECT 12 13 77: CONECT 13 14 14 15 77: CONECT 16 17 77: CONECT 17 18 20 77: CONECT 18 19 19 25 77: CONECT 20 21 77: CONECT 21 22 77: CONECT 22 23 23 24 77: CONECT 25 26 77: CONECT 26 27 77: CONECT 27 28 28 29 77: END 77: 77: Sequence: TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN 77: HELM: PEPTIDE1{T.T.C.C.P.S.I.V.A.R.S.N.F.N.V.C.R.L.P.G.T.P.E.A.I.C.A.T.Y.T.G.C.I.I.I.P.G.A.T.C.P.G.D.Y.A.N}$$$$ 77: Smiles: CC[C@H](C)[C@H](NC(=O)[C@H](C)NC(=O)[C@H](CCC(=O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CS)NC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@@H](N)[C@@H](C)O)[C@@H](C)O)[C@@H](C)CC)C(C)C)C(C)C)[C@@H](C)O)C(=O)N[C@@H](CS)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(N)=O)C(=O)O)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)O)[C@@H](C)O 77: PDB: 77: ATOM 1 N THR A 1 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 2 CA THR A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 3 C THR A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 4 O THR A 1 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 5 CB THR A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 6 OG1 THR A 1 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 7 CG2 THR A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 8 N THR A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 9 CA THR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 10 C THR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 11 O THR A 2 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 12 CB THR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 13 OG1 THR A 2 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 14 CG2 THR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 15 N CYS A 3 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 16 CA CYS A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 17 C CYS A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 18 O CYS A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 19 CB CYS A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 20 SG CYS A 3 0.000 0.000 0.000 1.00 0.00 S 77: ATOM 21 N CYS A 4 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 22 CA CYS A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 23 C CYS A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 24 O CYS A 4 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 25 CB CYS A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 26 SG CYS A 4 0.000 0.000 0.000 1.00 0.00 S 77: ATOM 27 N PRO A 5 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 28 CA PRO A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 29 C PRO A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 30 O PRO A 5 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 31 CB PRO A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 32 CG PRO A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 33 CD PRO A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 34 N SER A 6 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 35 CA SER A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 36 C SER A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 37 O SER A 6 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 38 CB SER A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 39 OG SER A 6 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 40 N ILE A 7 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 41 CA ILE A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 42 C ILE A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 43 O ILE A 7 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 44 CB ILE A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 45 CG1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 46 CG2 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 47 CD1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 48 N VAL A 8 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 49 CA VAL A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 50 C VAL A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 51 O VAL A 8 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 52 CB VAL A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 53 CG1 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 54 CG2 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 55 N ALA A 9 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 56 CA ALA A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 57 C ALA A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 58 O ALA A 9 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 59 CB ALA A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 60 N ARG A 10 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 61 CA ARG A 10 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 62 C ARG A 10 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 63 O ARG A 10 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 64 CB ARG A 10 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 65 CG ARG A 10 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 66 CD ARG A 10 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 67 NE ARG A 10 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 68 CZ ARG A 10 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 69 NH1 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 70 NH2 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 71 N SER A 11 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 72 CA SER A 11 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 73 C SER A 11 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 74 O SER A 11 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 75 CB SER A 11 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 76 OG SER A 11 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 77 N ASN A 12 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 78 CA ASN A 12 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 79 C ASN A 12 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 80 O ASN A 12 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 81 CB ASN A 12 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 82 CG ASN A 12 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 83 OD1 ASN A 12 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 84 ND2 ASN A 12 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 85 N PHE A 13 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 86 CA PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 87 C PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 88 O PHE A 13 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 89 CB PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 90 CG PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 91 CD1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 92 CD2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 93 CE1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 94 CE2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 95 CZ PHE A 13 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 96 N ASN A 14 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 97 CA ASN A 14 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 98 C ASN A 14 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 99 O ASN A 14 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 100 CB ASN A 14 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 101 CG ASN A 14 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 102 OD1 ASN A 14 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 103 ND2 ASN A 14 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 104 N VAL A 15 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 105 CA VAL A 15 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 106 C VAL A 15 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 107 O VAL A 15 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 108 CB VAL A 15 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 109 CG1 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 110 CG2 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 111 N CYS A 16 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 112 CA CYS A 16 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 113 C CYS A 16 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 114 O CYS A 16 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 115 CB CYS A 16 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 116 SG CYS A 16 0.000 0.000 0.000 1.00 0.00 S 77: ATOM 117 N ARG A 17 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 118 CA ARG A 17 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 119 C ARG A 17 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 120 O ARG A 17 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 121 CB ARG A 17 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 122 CG ARG A 17 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 123 CD ARG A 17 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 124 NE ARG A 17 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 125 CZ ARG A 17 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 126 NH1 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 127 NH2 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 128 N LEU A 18 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 129 CA LEU A 18 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 130 C LEU A 18 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 131 O LEU A 18 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 132 CB LEU A 18 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 133 CG LEU A 18 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 134 CD1 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 135 CD2 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 136 N PRO A 19 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 137 CA PRO A 19 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 138 C PRO A 19 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 139 O PRO A 19 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 140 CB PRO A 19 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 141 CG PRO A 19 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 142 CD PRO A 19 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 143 N GLY A 20 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 144 CA GLY A 20 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 145 C GLY A 20 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 146 O GLY A 20 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 147 N THR A 21 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 148 CA THR A 21 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 149 C THR A 21 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 150 O THR A 21 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 151 CB THR A 21 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 152 OG1 THR A 21 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 153 CG2 THR A 21 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 154 N PRO A 22 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 155 CA PRO A 22 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 156 C PRO A 22 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 157 O PRO A 22 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 158 CB PRO A 22 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 159 CG PRO A 22 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 160 CD PRO A 22 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 161 N GLU A 23 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 162 CA GLU A 23 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 163 C GLU A 23 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 164 O GLU A 23 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 165 CB GLU A 23 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 166 CG GLU A 23 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 167 CD GLU A 23 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 168 OE1 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 169 OE2 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 170 N ALA A 24 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 171 CA ALA A 24 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 172 C ALA A 24 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 173 O ALA A 24 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 174 CB ALA A 24 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 175 N ILE A 25 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 176 CA ILE A 25 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 177 C ILE A 25 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 178 O ILE A 25 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 179 CB ILE A 25 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 180 CG1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 181 CG2 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 182 CD1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 183 N CYS A 26 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 184 CA CYS A 26 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 185 C CYS A 26 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 186 O CYS A 26 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 187 CB CYS A 26 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 188 SG CYS A 26 0.000 0.000 0.000 1.00 0.00 S 77: ATOM 189 N ALA A 27 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 190 CA ALA A 27 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 191 C ALA A 27 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 192 O ALA A 27 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 193 CB ALA A 27 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 194 N THR A 28 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 195 CA THR A 28 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 196 C THR A 28 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 197 O THR A 28 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 198 CB THR A 28 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 199 OG1 THR A 28 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 200 CG2 THR A 28 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 201 N TYR A 29 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 202 CA TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 203 C TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 204 O TYR A 29 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 205 CB TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 206 CG TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 207 CD1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 208 CD2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 209 CE1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 210 CE2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 211 CZ TYR A 29 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 212 OH TYR A 29 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 213 N THR A 30 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 214 CA THR A 30 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 215 C THR A 30 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 216 O THR A 30 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 217 CB THR A 30 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 218 OG1 THR A 30 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 219 CG2 THR A 30 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 220 N GLY A 31 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 221 CA GLY A 31 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 222 C GLY A 31 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 223 O GLY A 31 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 224 N CYS A 32 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 225 CA CYS A 32 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 226 C CYS A 32 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 227 O CYS A 32 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 228 CB CYS A 32 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 229 SG CYS A 32 0.000 0.000 0.000 1.00 0.00 S 77: ATOM 230 N ILE A 33 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 231 CA ILE A 33 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 232 C ILE A 33 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 233 O ILE A 33 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 234 CB ILE A 33 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 235 CG1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 236 CG2 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 237 CD1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 238 N ILE A 34 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 239 CA ILE A 34 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 240 C ILE A 34 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 241 O ILE A 34 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 242 CB ILE A 34 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 243 CG1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 244 CG2 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 245 CD1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 246 N ILE A 35 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 247 CA ILE A 35 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 248 C ILE A 35 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 249 O ILE A 35 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 250 CB ILE A 35 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 251 CG1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 252 CG2 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 253 CD1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 254 N PRO A 36 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 255 CA PRO A 36 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 256 C PRO A 36 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 257 O PRO A 36 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 258 CB PRO A 36 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 259 CG PRO A 36 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 260 CD PRO A 36 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 261 N GLY A 37 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 262 CA GLY A 37 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 263 C GLY A 37 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 264 O GLY A 37 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 265 N ALA A 38 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 266 CA ALA A 38 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 267 C ALA A 38 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 268 O ALA A 38 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 269 CB ALA A 38 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 270 N THR A 39 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 271 CA THR A 39 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 272 C THR A 39 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 273 O THR A 39 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 274 CB THR A 39 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 275 OG1 THR A 39 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 276 CG2 THR A 39 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 277 N CYS A 40 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 278 CA CYS A 40 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 279 C CYS A 40 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 280 O CYS A 40 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 281 CB CYS A 40 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 282 SG CYS A 40 0.000 0.000 0.000 1.00 0.00 S 77: ATOM 283 N PRO A 41 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 284 CA PRO A 41 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 285 C PRO A 41 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 286 O PRO A 41 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 287 CB PRO A 41 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 288 CG PRO A 41 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 289 CD PRO A 41 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 290 N GLY A 42 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 291 CA GLY A 42 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 292 C GLY A 42 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 293 O GLY A 42 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 294 N ASP A 43 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 295 CA ASP A 43 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 296 C ASP A 43 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 297 O ASP A 43 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 298 CB ASP A 43 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 299 CG ASP A 43 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 300 OD1 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 301 OD2 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 302 N TYR A 44 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 303 CA TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 304 C TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 305 O TYR A 44 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 306 CB TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 307 CG TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 308 CD1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 309 CD2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 310 CE1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 311 CE2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 312 CZ TYR A 44 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 313 OH TYR A 44 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 314 N ALA A 45 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 315 CA ALA A 45 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 316 C ALA A 45 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 317 O ALA A 45 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 318 CB ALA A 45 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 319 N ASN A 46 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 320 CA ASN A 46 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 321 C ASN A 46 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 322 O ASN A 46 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 323 CB ASN A 46 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 324 CG ASN A 46 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 325 OD1 ASN A 46 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 326 ND2 ASN A 46 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 327 OXT ASN A 46 0.000 0.000 0.000 1.00 0.00 O 77: CONECT 1 2 77: CONECT 2 3 5 77: CONECT 3 4 4 8 77: CONECT 5 6 7 77: CONECT 8 9 77: CONECT 9 10 12 77: CONECT 10 11 11 15 77: CONECT 12 13 14 77: CONECT 15 16 77: CONECT 16 17 19 77: CONECT 17 18 18 21 77: CONECT 19 20 77: CONECT 21 22 77: CONECT 22 23 25 77: CONECT 23 24 24 27 77: CONECT 25 26 77: CONECT 27 28 33 77: CONECT 28 29 31 77: CONECT 29 30 30 34 77: CONECT 31 32 77: CONECT 32 33 77: CONECT 34 35 77: CONECT 35 36 38 77: CONECT 36 37 37 40 77: CONECT 38 39 77: CONECT 40 41 77: CONECT 41 42 44 77: CONECT 42 43 43 48 77: CONECT 44 45 46 77: CONECT 46 47 77: CONECT 48 49 77: CONECT 49 50 52 77: CONECT 50 51 51 55 77: CONECT 52 53 54 77: CONECT 55 56 77: CONECT 56 57 59 77: CONECT 57 58 58 60 77: CONECT 60 61 77: CONECT 61 62 64 77: CONECT 62 63 63 71 77: CONECT 64 65 77: CONECT 65 66 77: CONECT 66 67 77: CONECT 67 68 77: CONECT 68 69 69 70 77: CONECT 71 72 77: CONECT 72 73 75 77: CONECT 73 74 74 77 77: CONECT 75 76 77: CONECT 77 78 77: CONECT 78 79 81 77: CONECT 79 80 80 85 77: CONECT 81 82 77: CONECT 82 83 83 84 77: CONECT 85 86 77: CONECT 86 87 89 77: CONECT 87 88 88 96 77: CONECT 89 90 77: CONECT 90 91 91 92 77: CONECT 91 93 77: CONECT 92 94 94 77: CONECT 93 95 95 77: CONECT 94 95 77: CONECT 96 97 77: CONECT 97 98 100 77: CONECT 98 99 99 104 77: CONECT 100 101 77: CONECT 101 102 102 103 77: CONECT 104 105 77: CONECT 105 106 108 77: CONECT 106 107 107 111 77: CONECT 108 109 110 77: CONECT 111 112 77: CONECT 112 113 115 77: CONECT 113 114 114 117 77: CONECT 115 116 77: CONECT 117 118 77: CONECT 118 119 121 77: CONECT 119 120 120 128 77: CONECT 121 122 77: CONECT 122 123 77: CONECT 123 124 77: CONECT 124 125 77: CONECT 125 126 126 127 77: CONECT 128 129 77: CONECT 129 130 132 77: CONECT 130 131 131 136 77: CONECT 132 133 77: CONECT 133 134 135 77: CONECT 136 137 142 77: CONECT 137 138 140 77: CONECT 138 139 139 143 77: CONECT 140 141 77: CONECT 141 142 77: CONECT 143 144 77: CONECT 144 145 77: CONECT 145 146 146 147 77: CONECT 147 148 77: CONECT 148 149 151 77: CONECT 149 150 150 154 77: CONECT 151 152 153 77: CONECT 154 155 160 77: CONECT 155 156 158 77: CONECT 156 157 157 161 77: CONECT 158 159 77: CONECT 159 160 77: CONECT 161 162 77: CONECT 162 163 165 77: CONECT 163 164 164 170 77: CONECT 165 166 77: CONECT 166 167 62/230 Test #71: testMolSupplier ........................ Passed 0.45 sec test 82 Start 82: cdxmlParserCatchTest 82: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 82: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 82: Test timeout computed to be: 1500 77: CONECT 167 168 168 169 77: CONECT 170 171 77: CONECT 171 172 174 77: CONECT 172 173 173 175 77: CONECT 175 176 77: CONECT 176 177 179 77: CONECT 177 178 178 183 77: CONECT 179 180 181 77: CONECT 181 182 77: CONECT 183 184 77: CONECT 184 185 187 77: CONECT 185 186 186 189 77: CONECT 187 188 77: CONECT 189 190 77: CONECT 190 191 193 77: CONECT 191 192 192 194 77: CONECT 194 195 77: CONECT 195 196 198 77: CONECT 196 197 197 201 77: CONECT 198 199 200 77: CONECT 201 202 77: CONECT 202 203 205 77: CONECT 203 204 204 213 77: CONECT 205 206 77: CONECT 206 207 207 208 77: CONECT 207 209 77: CONECT 208 210 210 77: CONECT 209 211 211 77: CONECT 210 211 77: CONECT 211 212 77: CONECT 213 214 77: CONECT 214 215 217 77: CONECT 215 216 216 220 77: CONECT 217 218 219 77: CONECT 220 221 77: CONECT 221 222 77: CONECT 222 223 223 224 77: CONECT 224 225 77: CONECT 225 226 228 77: CONECT 226 227 227 230 77: CONECT 228 229 77: CONECT 230 231 77: CONECT 231 232 234 77: CONECT 232 233 233 238 77: CONECT 234 235 236 77: CONECT 236 237 77: CONECT 238 239 77: CONECT 239 240 242 77: CONECT 240 241 241 246 77: CONECT 242 243 244 77: CONECT 244 245 77: CONECT 246 247 77: CONECT 247 248 250 77: CONECT 248 249 249 254 77: CONECT 250 251 252 77: CONECT 252 253 77: CONECT 254 255 260 77: CONECT 255 256 258 77: CONECT 256 257 257 261 77: CONECT 258 259 77: CONECT 259 260 77: CONECT 261 262 77: CONECT 262 263 77: CONECT 263 264 264 265 77: CONECT 265 266 77: CONECT 266 267 269 77: CONECT 267 268 268 270 77: CONECT 270 271 77: CONECT 271 272 274 77: CONECT 272 273 273 277 77: CONECT 274 275 276 77: CONECT 277 278 77: CONECT 278 279 281 77: CONECT 279 280 280 283 77: CONECT 281 282 77: CONECT 283 284 289 77: CONECT 284 285 287 77: CONECT 285 286 286 290 77: CONECT 287 288 77: CONECT 288 289 77: CONECT 290 291 77: CONECT 291 292 77: CONECT 292 293 293 294 77: CONECT 294 295 77: CONECT 295 296 298 77: CONECT 296 297 297 302 77: CONECT 298 299 77: CONECT 299 300 300 301 77: CONECT 302 303 77: CONECT 303 304 306 77: CONECT 304 305 305 314 77: CONECT 306 307 77: CONECT 307 308 308 309 77: CONECT 308 310 77: CONECT 309 311 311 77: CONECT 310 312 312 77: CONECT 311 312 77: CONECT 312 313 77: CONECT 314 315 77: CONECT 315 316 318 77: CONECT 316 317 317 319 77: CONECT 319 320 77: CONECT 320 321 323 77: CONECT 321 322 322 327 77: CONECT 323 324 77: CONECT 324 325 325 326 77: END 77: 77: Sequence: GREG 77: HELM: PEPTIDE1{G.R.E.G}$$$$ 77: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 77: PDB: 77: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 77: CONECT 1 2 77: CONECT 2 3 77: CONECT 3 4 4 5 77: CONECT 5 6 77: CONECT 6 7 9 77: CONECT 7 8 8 16 77: CONECT 9 10 77: CONECT 10 11 77: CONECT 11 12 77: CONECT 12 13 77: CONECT 13 14 14 15 77: CONECT 16 17 77: CONECT 17 18 20 77: CONECT 18 19 19 25 77: CONECT 20 21 77: CONECT 21 22 77: CONECT 22 23 23 24 77: CONECT 25 26 77: CONECT 26 27 77: CONECT 27 28 28 29 77: END 77: 77: Sequence: CYIQNCPLG 77: HELM: PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$ 77: Smiles: CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccc(O)cc2)NC(=O)[C@@H](N)CSSC[C@@H](C(=O)N2CCC[C@H]2C(=O)N[C@@H](CC(C)C)C(=O)NCC(N)=O)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(N)=O)NC1=O 77: PDB: 77: ATOM 1 N CYS A 1 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 2 CA CYS A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 3 C CYS A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 4 O CYS A 1 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 5 CB CYS A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 6 SG CYS A 1 0.000 0.000 0.000 1.00 0.00 S 77: ATOM 7 N TYR A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 8 CA TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 9 C TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 10 O TYR A 2 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 11 CB TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 12 CG TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 13 CD1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 14 CD2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 15 CE1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 16 CE2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 17 CZ TYR A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 18 OH TYR A 2 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 19 N ILE A 3 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 20 CA ILE A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 21 C ILE A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 22 O ILE A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 23 CB ILE A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 24 CG1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 25 CG2 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 26 CD1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 27 N GLN A 4 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 28 CA GLN A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 29 C GLN A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 30 O GLN A 4 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 31 CB GLN A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 38 C ASN A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 39 O ASN A 5 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 40 CB ASN A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 41 CG ASN A 5 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 42 OD1 ASN A 5 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 43 ND2 ASN A 5 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 44 N CYS A 6 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 45 CA CYS A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 46 C CYS A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 47 O CYS A 6 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 48 CB CYS A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 49 SG CYS A 6 0.000 0.000 0.000 1.00 0.00 S 77: ATOM 50 N PRO A 7 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 51 CA PRO A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 52 C PRO A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 53 O PRO A 7 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 54 CB PRO A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 55 CG PRO A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 56 CD PRO A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 57 N LEU A 8 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 58 CA LEU A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 59 C LEU A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 60 O LEU A 8 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 61 CB LEU A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 62 CG LEU A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 63 CD1 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 64 CD2 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 65 N GLY A 9 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 66 CA GLY A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 67 C GLY A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 68 O GLY A 9 0.000 0.000 0.000 1.00 0.00 O 77: HETATM 69 N NH2 A 10 0.000 0.000 0.000 1.00 0.00 N 77: CONECT 1 2 77: CONECT 2 3 5 77: CONECT 3 4 4 7 77: CONECT 5 6 77: CONECT 6 49 77: CONECT 7 8 77: CONECT 8 9 11 77: CONECT 9 10 10 19 77: CONECT 11 12 77: CONECT 12 13 13 14 77: CONECT 13 15 77: CONECT 14 16 16 77: CONECT 15 17 17 77: CONECT 16 17 77: CONECT 17 18 77: CONECT 19 20 77: CONECT 20 21 23 77: CONECT 21 22 22 27 77: CONECT 23 24 25 77: CONECT 25 26 77: CONECT 27 28 77: CONECT 28 29 31 77: CONECT 29 30 30 36 77: CONECT 31 32 77: CONECT 32 33 77: CONECT 33 34 34 35 77: CONECT 36 37 77: CONECT 37 38 40 77: CONECT 38 39 39 44 77: CONECT 40 41 77: CONECT 41 42 42 43 77: CONECT 44 45 77: CONECT 45 46 48 77: CONECT 46 47 47 50 77: CONECT 48 49 77: CONECT 50 51 56 77: CONECT 51 52 54 77: CONECT 52 53 53 57 77: CONECT 54 55 77: CONECT 55 56 77: CONECT 57 58 77: CONECT 58 59 61 77: CONECT 59 60 60 65 77: CONECT 61 62 77: CONECT 62 63 64 77: CONECT 65 66 77: CONECT 66 67 77: CONECT 67 68 68 69 77: END 77: 77: Sequence: LfPVXLfPVX 77: HELM: PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$ 77: Smiles: CC(C)C[C@@H]1NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC1=O 77: PDB: 77: ATOM 1 N LEU A 1 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 2 CA LEU A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 3 C LEU A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 4 O LEU A 1 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 5 CB LEU A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 6 CG LEU A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 7 CD1 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 8 CD2 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 9 N DPN A 2 0.000 0.000 0.000 1.00 0.00 N 77: HETATM 10 CA DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 11 C DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 12 O DPN A 2 0.000 0.000 0.000 1.00 0.00 O 77: HETATM 13 CB DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 14 CG DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 15 CD1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 16 CD2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 17 CE1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 18 CE2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 19 CZ DPN A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 20 N PRO A 3 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 21 CA PRO A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 22 C PRO A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 23 O PRO A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 24 CB PRO A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 25 CG PRO A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 26 CD PRO A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 27 N VAL A 4 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 28 CA VAL A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 29 C VAL A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 30 O VAL A 4 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 31 CB VAL A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 32 CG1 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 33 CG2 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 34 N ORN A 5 0.000 0.000 0.000 1.00 0.00 N 77: HETATM 35 CA ORN A 5 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 36 C ORN A 5 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 37 O ORN A 5 0.000 0.000 0.000 1.00 0.00 O 77: HETATM 38 CB ORN A 5 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 39 CG ORN A 5 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 40 CD ORN A 5 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 41 NE ORN A 5 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 42 N LEU A 6 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 43 CA LEU A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 44 C LEU A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 45 O LEU A 6 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 46 CB LEU A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 47 CG LEU A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N 77: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O 77: HETATM 54 CB DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 55 CG DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 56 CD1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 57 CD2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 58 CE1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 59 CE2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 60 CZ DPN A 7 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 61 N PRO A 8 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 62 CA PRO A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 63 C PRO A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 64 O PRO A 8 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 65 CB PRO A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 66 CG PRO A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 67 CD PRO A 8 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 68 N VAL A 9 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 69 CA VAL A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 70 C VAL A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 71 O VAL A 9 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 72 CB VAL A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 73 CG1 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 74 CG2 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 75 N ORN A 10 0.000 0.000 0.000 1.00 0.00 N 77: HETATM 76 CA ORN A 10 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 77 C ORN A 10 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 78 O ORN A 10 0.000 0.000 0.000 1.00 0.00 O 77: HETATM 79 CB ORN A 10 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 80 CG ORN A 10 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 81 CD ORN A 10 0.000 0.000 0.000 1.00 0.00 C 77: HETATM 82 NE ORN A 10 0.000 0.000 0.000 1.00 0.00 N 77: CONECT 1 2 77 77: CONECT 2 3 5 77: CONECT 3 4 4 9 77: CONECT 5 6 77: CONECT 6 7 8 77: CONECT 9 10 77: CONECT 10 11 13 77: CONECT 11 12 12 20 77: CONECT 13 14 77: CONECT 14 15 15 16 77: CONECT 15 17 77: CONECT 16 18 18 77: CONECT 17 19 19 77: CONECT 18 19 77: CONECT 20 21 26 77: CONECT 21 22 24 77: CONECT 22 23 23 27 77: CONECT 24 25 77: CONECT 25 26 77: CONECT 27 28 77: CONECT 28 29 31 77: CONECT 29 30 30 34 77: CONECT 31 32 33 77: CONECT 34 35 77: CONECT 35 36 38 77: CONECT 36 37 37 42 77: CONECT 38 39 77: CONECT 39 40 77: CONECT 40 41 77: CONECT 42 43 77: CONECT 43 44 46 77: CONECT 44 45 45 50 77: CONECT 46 47 77: CONECT 47 48 49 77: CONECT 50 51 77: CONECT 51 52 54 77: CONECT 52 53 53 61 77: CONECT 54 55 77: CONECT 55 56 56 57 77: CONECT 56 58 77: CONECT 57 59 59 77: CONECT 58 60 60 77: CONECT 59 60 77: CONECT 61 62 67 77: CONECT 62 63 65 77: CONECT 63 64 64 68 77: CONECT 65 66 77: CONECT 66 67 77: CONECT 68 69 77: CONECT 69 70 72 77: CONECT 70 71 71 75 77: CONECT 72 73 74 77: CONECT 75 76 77: CONECT 76 77 79 77: CONECT 77 78 78 77: CONECT 79 80 77: CONECT 80 81 77: CONECT 81 82 77: END 77: 77: Sequence: GREG 77: HELM: PEPTIDE1{G.R.E.G}$$$$ 77: Smiles: N=C(N)NCCCC(NC(=O)CN)C(=O)NC(CCC(=O)O)C(=O)NCC(=O)O 77: PDB: 77: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 23 OD1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 24 OD2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 77: CONECT 1 2 77: CONECT 2 3 77: CONECT 3 4 4 5 77: CONECT 5 6 77: CONECT 6 7 9 77: CONECT 7 8 8 16 77: CONECT 9 10 77: CONECT 10 11 77: CONECT 11 12 77: CONECT 12 13 77: CONECT 13 14 14 15 77: CONECT 16 17 77: CONECT 17 18 20 77: CONECT 18 19 19 25 77: CONECT 20 21 77: CONECT 21 22 77: CONECT 22 23 23 24 77: CONECT 25 26 77: CONECT 26 27 77: CONECT 27 28 28 29 77: END 77: 63/230 Test #69: testAtropisomers ....................... Passed 0.60 sec 79: Randomness seeded to: 4219103258 79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 79: [09:08:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 79: [09:08:14] SGroup 1 is invalid and will be ignored 79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 79: [09:08:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 79: [09:08:14] SGroup 1 is invalid and will be ignored 79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 79: [09:08:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 79: [09:08:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 79: [09:08:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 79: [09:08:14] SGroup 1 is invalid and will be ignored 79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 79: [09:08:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 79: [09:08:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 79: [09:08:14] SGroup 1 is invalid and will be ignored 79: [09:08:14] SGroup 3 referenced on line 40 not found. 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: no bonds 79: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp 79: Failed Expression: !d_bonds.empty() 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# 0x00007F6D888DA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# 0x0000557D532D1529 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 16# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] SGroup 3 referenced on line 40 not found. 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: no bonds 79: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp 79: Failed Expression: !d_bonds.empty() 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# 0x00007F6D888DA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# 0x0000557D532D15D2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 16# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] no bonds 79: [09:08:14] SGroup 1 is invalid and will be ignored 79: [09:08:14] SGroup line too short: 'M SBV 1 6' on line 42 79: [09:08:14] SGroup 1 is invalid and will be ignored 79: [09:08:14] SGroup line too short: 'M SBL 2 3 9 10' on line 46 79: [09:08:14] SGroup 2 is invalid and will be ignored 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_bondBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888D9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# 0x0000557D532D2192 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_bondBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888D9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# 0x0000557D532D223A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] bookmark not found 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bond is not part of the SubstanceGroup 79: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp 79: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888DA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# 0x0000557D532D223A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] bond is not part of the SubstanceGroup 79: [09:08:14] SGroup 2 is invalid and will be ignored 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_atomBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888D9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# 0x0000557D532D25A9 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_atomBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888D9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# 0x0000557D532D2651 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] bookmark not found 79: [09:08:14] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. 79: [09:08:14] SGroup 2 is invalid and will be ignored 79: [09:08:14] WARNING: final character of V3000 array is not ')' 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_bondBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532CFEB3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] WARNING: final character of V3000 array is not ')' 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_bondBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532CFF4B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] bookmark not found 79: [09:08:14] SGroup 1 is invalid and will be ignored 79: [09:08:14] WARNING: final character of V3000 array is not ')' 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_atomBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532D02B4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] WARNING: final character of V3000 array is not ')' 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_atomBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532D034C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] bookmark not found 79: [09:08:14] SGroup 1 is invalid and will be ignored 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_bondBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532D06B3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_bondBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532D074C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] bookmark not found 79: [09:08:14] SGroup 2 is invalid and will be ignored 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_atomBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532D0AB2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: (lu != d_atomBookmarks.end()) 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532D0B4C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] bookmark not found 79: [09:08:14] SGroup 2 is invalid and will be ignored 79: [09:08:14] Explicit valence for atom # 2 O, 3, is greater than permitted 79: [09:08:14] Explicit valence for atom # 1 O, 3, is greater than permitted 79: [09:08:14] Explicit valence for atom # 1 C, 5, is greater than permitted 79: [09:08:14] sanitize [09:08:14] UNK: [09:08:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 79: [09:08:14] skipping block at line 7: 'BEGIN ATOM' 79: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 79: END 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: no stream 79: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp 79: Failed Expression: dp_inStream 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 4# 0x0000557D532C0B3D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: no stream 79: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp 79: Failed Expression: dp_inStream 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 4# 0x0000557D532C0D18 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 81: Randomness seeded to: 929538344 81: =============================================================================== 81: All tests passed (100 assertions in 2 test cases) 81: 64/230 Test #77: testSequence ........................... Passed 0.14 sec 65/230 Test #81: XYZFileParserCatchTest ................. Passed 0.08 sec test 83 Start 83: molfileStereoCatchTest 83: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest 83: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 83: Test timeout computed to be: 1500 test 84 Start 84: connectTheDotsTest 84: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 84: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 84: Test timeout computed to be: 1500 test 85 Start 85: v2MolSuppliers 85: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers 85: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 85: Test timeout computed to be: 1500 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: no stream 79: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp 79: Failed Expression: dp_inStream 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 4# 0x0000557D532C1151 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: no stream 79: Violation occurred on line 264 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp 79: Failed Expression: dp_inStream 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 4# 0x0000557D532C14D6 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: no stream 79: Violation occurred on line 577 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 79: Failed Expression: dp_sInStream != nullptr 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 4# 0x0000557D532C1753 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 21 79: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 20 79: [09:08:14] BEGIN SGROUP line not found on line 14 79: [09:08:14] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. 79: [09:08:14] END SGROUP line not found on line 14 79: [09:08:14] END SGROUP line not found on line 14 79: [09:08:14] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. 79: [09:08:14] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. 79: [09:08:14] 79: 79: **** 79: Range Error 79: idx 79: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp 79: Failed Expression: 99 < 9 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# 0x0000557D5330521F in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 7# 0x0000557D532C6B53 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 16# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. 79: [09:08:14] Multiple ATTCHPT values for atom 2 on line 9 79: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 12 79: [09:08:14] SMARTS Parse Error: syntax error while parsing: [#6;R 79: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' 79: [09:08:14] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. 79: [09:08:14] Skipping empty SMARTS value for SMARTSQ. 79: [09:08:14] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. 79: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 12 79: [09:08:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 79: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: [09:08:14] WARNING: Skipping property bar because the value includes an illegal blank line 79: [09:08:14] WARNING: Skipping property baz because the value includes an illegal blank line 79: [09:08:14] WARNING: Skipping property bletch 79: nope because the name includes a newline 79: [09:08:14] WARNING: Skipping property bletch 79: nope2 because the name includes a newline 79: [09:08:14] 79: 79: **** 79: Post-condition Violation 79: Element 'QQQ' not found 79: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 79: Failed Expression: anum > -1 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x00007F6D888C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# 0x00007F6D888D32F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888D47CD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532992FC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Post-condition Violation 79: Element 'QQQ' not found 79: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 79: Failed Expression: anum > -1 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x00007F6D888C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# 0x00007F6D888D32F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888D47CD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532989DA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Post-condition Violation 79: Element 'QQQ' not found 79: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 79: Failed Expression: anum > -1 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x00007F6D888C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# 0x00007F6D888D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D532992A4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Post-condition Violation 79: Element 'QQQ' not found 79: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 79: Failed Expression: anum > -1 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# 0x00007F6D888C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# 0x00007F6D888D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# 0x00007F6D888D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 9# 0x0000557D53298F42 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] atom 3 has a negative isotope value. line: 15 80: Randomness seeded to: 1628274664 80: =============================================================================== 80: All tests passed (95 assertions in 4 test cases) 80: 66/230 Test #80: testPropertyLists ...................... Passed 0.14 sec 74: [09:08:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 74: 0.40201265 0.40201265 74: -0.13299436 -0.13299436 74: 1.00000017 1.00000017 74: 0.8762226 0.8762226 74: 0.9973909 0.9973909 74: 1.00000003 1.00000003 74: 0.36613799 0.36613799 74: 2.1107185 2.1107185 74: 0.99999982 0.99999982 74: 2.48696157 2.48696157 74: 1.00479935 1.00479935 74: 0.99999999 0.99999999 74: 3.03311841 3.03311841 74: 2.23739955 2.23739955 74: 1.0000001 1.0000001 74: 3.00772337 3.00772337 74: 0.37399294 0.37399294 74: 2.07713325 2.07713325 74: 3.0077234 3.0077234 74: 0.37399312 0.37399312 74: -0.07713336 -0.07713336 74: [09:08:14] bond with order 0 found on line 11. This is not part of the MDL specification. 74: [09:08:14] bond with order 0 found on line 16. This is not part of the MDL specification. 82: Randomness seeded to: 1667303315 82: [09:08:14] Invalid or missing fragment id from CDXML fragment, assigning new one... 82: [09:08:14] Explicit valence for atom # 3 N, 4, is greater than permitted 82: [09:08:14] CDXMLParser: failed sanitizing skipping fragment 32 82: [09:08:14] Bad bond in CDXML skipping fragment 58... 82: [09:08:14] Invalid or missing fragment id from CDXML fragment, assigning new one... test 86 Start 86: v2FileParsersCatchTest 86: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest 86: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 86: Test timeout computed to be: 1500 79: [09:08:14] 79: 79: **** 79: Invariant Violation 79: bad prop value 79: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 79: Failed Expression: nSwaps < 2 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# 0x00007F6D88994AA4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 5# 0x0000557D532DA1FC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 6# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 7# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 12# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 14# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 79: [09:08:14] 79: 79: **** 79: Pre-condition Violation 79: no input stream 79: Violation occurred on line 544 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 79: Failed Expression: dp_sInStream 79: ---------- 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# 0x0000557D532DA686 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: 82: [09:08:14] Bad bond in CDXML skipping fragment 58... 67/230 Test #74: testMolWriter .......................... Passed 0.49 sec test 87 Start 87: multithreadedSupplierCatchTest 87: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest 87: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 87: Test timeout computed to be: 1500 84: Randomness seeded to: 4243776243 84: =============================================================================== 84: All tests passed (8 assertions in 1 test case) 84: 83: Randomness seeded to: 2793746775 83: [09:08:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 83: [09:08:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 83: [09:08:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 83: [09:08:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 83: =============================================================================== 83: All tests passed (142 assertions in 6 test cases) 83: 68/230 Test #83: molfileStereoCatchTest ................. Passed 0.08 sec 69/230 Test #84: connectTheDotsTest ..................... Passed 0.05 sec test 88 Start 88: testSubstructMatch 88: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct 88: Test timeout computed to be: 1500 test 89 Start 89: substructTestCatch 89: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 89: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct 89: Test timeout computed to be: 1500 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 86: Randomness seeded to: 1205933431 86: =============================================================================== 86: All tests passed (6 assertions in 1 test case) 86: 85: Randomness seeded to: 4095904522 85: =============================================================================== 85: All tests passed (12 assertions in 5 test cases) 85: 88: ----------------- Test 1 88: Done 88: 88: ----------------- Test 2 88: Done 88: 88: ----------------- Test 3 88: Done 88: 88: ----------------- Test 4 88: Done 88: 88: ----------------- Test 5 88: Done 88: 88: ----------------- Test 5 QueryRoot 88: Done 88: 88: ----------------- Test 6 (Issue71 related) 88: Done 88: 88: ----------------- Testing serial numbers on recursive queries 88: Done 88: 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test multithreading 88: reading molecules 70/230 Test #86: v2FileParsersCatchTest ................. Passed 0.06 sec test 90 Start 90: testGenericGroups 90: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 90: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups 90: Test timeout computed to be: 1500 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] WARNING: not removing hydrogen atom without neighbors 82: [09:08:14] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. 34: [09:08:14] Maximum BFS search size exceeded. 34: This is likely due to a highly symmetric fused ring system. 71/230 Test #85: v2MolSuppliers ......................... Passed 0.10 sec test 91 Start 91: testReaction 91: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 91: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 91: Test timeout computed to be: 1500 82: [09:08:14] Incomplete atom labelling, cannot make bond 82: [09:08:14] Incomplete atom labelling, cannot make bond 79: [09:08:14] ERROR: molecules without atoms cannot be exported to Maestro files. 79: [09:08:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 79: [09:08:14] ERROR: the mol cannot be kekulized, and will not be written to the output file. 79: [09:08:14] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. 88: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 88: processing 88: launch :0 88: launch :1 88: launch :2 88: launch :3 34: F/C=C/Cl 34: [H]/C(F)=C(/[H])Cl 34: F/C=C/Cl 34: F/C=C/Cl 34: C/C(F)=C(/C)Cl 82: [09:08:14] Incomplete atom labelling, cannot make bond 79: [09:08:14] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[09:08:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 79: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: [09:08:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 79: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 34: [09:08:14] ----------------------- 34: Testing isRingFused 82: [09:08:14] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 82: [09:08:14] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 82: [09:08:14] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast 82: [09:08:14] Failed to parse XML fragment 5 node: b attribute: Order: 5 82: [09:08:14] Invalid or missing fragment id from CDXML fragment, assigning new one... 72/230 Test #34: graphmolMolOpsTest ..................... Passed 1.52 sec test 92 Start 92: testReactionFingerprints 92: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 92: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 92: Test timeout computed to be: 1500 82: =============================================================================== 82: All tests passed (263 assertions in 7 test cases) 82: 73/230 Test #82: cdxmlParserCatchTest ................... Passed 0.27 sec test 93 Start 93: testEnumeration 93: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 93: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 93: Test timeout computed to be: 1500 91: smi: O=C1CNC(=O)CN1 91: 1: O=C1CNC(=O)CN1 91: 2: COOC 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 91: O=C1CNC(=O)CN1 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 91: [09:08:14] atom 0 in product 0 has multiple charge specifications. 91: mass: 15.0001 92: [09:08:14] ------------------------------------- 92: [09:08:14] Test Reaction StructuralFingerprint 91: Oc1ccccn1 91: Oc1ccc[nH]1 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: ([C:2] 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [C:2]) 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' 91: [09:08:14] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 91: [09:08:14] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 91: [09:08:14] reactant 2 has no mapped atoms. 91: [09:08:14] >> Atoms within one molecule have different RXN roles. 91: [09:08:14] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: ([C:2] 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' 91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] 91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' 91: [09:08:14] reactant 0 has no mapped atoms. 91: [09:08:14] reactant 1 has no mapped atoms. 91: [09:08:14] reactant 3 has no mapped atoms. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 5 found multiple times. 91: [09:08:14] product atom-mapping number 6 found multiple times. 91: [09:08:14] product atom-mapping number 7 found multiple times. 91: [09:08:14] product atom-mapping number 8 found multiple times. 91: [09:08:14] product atom-mapping number 12 found multiple times. 91: [09:08:14] product atom-mapping number 9 found multiple times. 91: [09:08:14] product atom-mapping number 10 found multiple times. 91: [09:08:14] product atom-mapping number 11 found multiple times. 91: [09:08:14] reactant 0 has no mapped atoms. 91: [09:08:14] reactant 1 has no mapped atoms. 91: [09:08:14] reactant 3 has no mapped atoms. 91: [09:08:14] reactant atom-mapping number 19 found multiple times. 91: [09:08:14] reactant atom-mapping number 25 found multiple times. 91: [09:08:14] reactant atom-mapping number 20 found multiple times. 91: [09:08:14] reactant atom-mapping number 21 found multiple times. 91: [09:08:14] reactant atom-mapping number 22 found multiple times. 91: [09:08:14] reactant atom-mapping number 23 found multiple times. 91: [09:08:14] reactant atom-mapping number 24 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 91: [09:08:14] product atom-mapping number 5 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 5 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 91: [09:08:14] product atom-mapping number 5 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 5 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: F[C@@](Cl)(Br)O[C@](F)(Cl)Br 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: F[C@](Cl)(Br)O[C@](F)(Cl)Br 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 4 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 91: [09:08:14] product atom-mapping number 3 found multiple times. 91: [09:08:14] product atom-mapping number 2 found multiple times. 91: [09:08:14] product atom-mapping number 1 found multiple times. 91: [09:08:14] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 91: [09:08:14] product atom-mapping number 6 not found in reactants. 91: [09:08:14] product atom-mapping number 7 not found in reactants. 91: [09:08:14] product atom-mapping number 8 not found in reactants. 91: [09:08:14] product atom-mapping number 7 not found in reactants. 91: [09:08:14] product atom-mapping number 8 not found in reactants. 91: [09:08:14] product atom-mapping number 9 not found in reactants. 91: [09:08:14] product atom-mapping number 10 not found in reactants. 91: [09:08:14] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 6 91: [09:08:14] product atom-mapping number 7 not found in reactants. 91: [09:08:14] product atom-mapping number 8 not found in reactants. 91: [09:08:14] product atom-mapping number 9 not found in reactants. 91: [09:08:14] product atom-mapping number 10 not found in reactants. 91: [09:08:14] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 6 92: [09:08:14] ------------------------------------- 92: [09:08:14] Test Reaction DifferenceFingerprint 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 91: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 91: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 74/230 Test #92: testReactionFingerprints ............... Passed 0.10 sec test 94 Start 94: rxnTestCatch 94: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 94: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 94: Test timeout computed to be: 1500 67: Test 67: 67: badWedgeError.sdf 67: 67: Test 67: 67: CrossedDoubleBondWithChiralNbr2.sdf 67: 67: Test 67: 67: CrossedDoubleBondWithChiralNbr.sdf 67: 67: Test 67: 67: SimpleWiggleDoubleBond.sdf 67: 67: Test 67: 67: lostStereoAnd.sdf 67: 67: Test 67: 67: DoubleBondChain.sdf 67: 67: Test 67: 67: UnitsError.sdf 67: 67: Test 67: 67: StarAtom.sdf 67: 67: Test 67: 67: nonProprietary.mol 67: 67: Test 67: 67: ChiralTest.sdf 67: 67: Test 67: 67: TestBond1.mol 67: 67: Test 67: 67: Sgroup_MUL_ParentInMiddle.sdf 67: 67: Test 67: 67: BadRxn.rxn 67: 67: Test 67: 67: FalseChiral.mrv 67: 67: Test 67: 67: FalseChiral.mrv 67: 67: Test 67: 67: Cubane.mrv 67: 67: Test 67: 67: NewChiralTest.mrv 67: 67: Test 67: 67: NewChiralTest.mrv 67: 67: Test 67: 67: NewChiralTestNoChiral.mrv 67: 67: Test 67: 67: NewChiralTestNoChiral.mrv 67: 67: Test 67: 67: NewChiralTestAllChiral.mrv 67: 67: Test 67: 67: NewChiralTestAllChiral.mrv 67: 67: Test 67: 67: DataSgroupMissingUnitsDisplayed.mrv 67: 67: Test 67: 67: lostStereoAnd.mrv 67: 67: Test 67: 67: DoubleBondChain.mrv 67: 67: Test 67: 67: WigglyAndCrossed.mrv 67: 67: Test 67: 67: BondTypes.mrv 67: 67: Test 67: 67: EmbeddedSGroupSUP_MUL.mrv 67: 67: Test 67: 67: EmbeddedSgroupCOP_SUP.mrv 67: 67: Test 67: 67: EmbeddedSgroupDAT_SUP.mrv 67: 67: Test 67: 67: EmbeddedSgroupMULTICENTER_SUP.mrv 67: 67: Test 67: 67: EmbeddedSgroupMUL_MUL.mrv 67: 67: Test 67: 67: EmbeddedSgroupMUL_MUL2.mrv 67: 67: Test 67: 67: EmbeddedSgroupMUL_SUP.mrv 67: 67: Test 67: 67: EmbeddedSgroupSRU_SUP.mrv 67: 67: Test 67: 67: EmbeddedSgroupSUPEXP_SUP.mrv 67: 67: Test 67: 67: EmbeddedSgroupSUPEXP_SUP2.mrv 67: 67: Test 67: 67: EmbeddedSgroupSUP_MULTICENTER.mrv 67: 67: Test 67: 67: EmbeddedSgroupSUP_SUP.mrv 67: 67: Test 67: 67: EmbeddedSgroupSUP_SUP2.mrv 67: 67: Test 67: 67: RgroupBad.mrv 67: 67: Test 67: 67: valenceLessThanDrawn.mrv 67: 67: Test 67: 67: data_sgroup_no_fieldname.mrv 67: 67: Test 67: 67: data_sgroup_empty_field_data.mrv 67: 67: Test 67: 67: radical_value.mrv 67: 67: Test 67: 67: emptyOneLineAtomList.mrv 67: 67: Test 67: 67: mrvValence_value.mrv 67: 67: Test 67: 67: ChiralTest2.mrv 67: 67: Test 67: 67: ChiralTest.mrv 67: 67: Test 67: 67: SnCl2.mrv 67: 67: Test 67: 67: SnH2Cl2.mrv 67: 67: Test 67: 67: marvin01.mrv 67: 67: Test 67: 67: marvin02.mrv 67: 67: Test 67: 67: marvin07.mrv 67: 67: Test 67: 67: marvin10.mrv 67: 67: Test 67: 67: marvin06.mrv 67: 67: Test 67: 67: marvin12.mrv 67: 67: Test 67: 67: EmptyMol.mrv 67: 67: Test 67: 67: Sparse.mrv 67: 67: Test 67: 67: Sparse2.mrv 67: 67: Test 67: 67: Sparse3.mrv 67: 67: Test 67: 67: MarvinNoCoords.mrv 67: 67: Test 67: 67: aspirin.mrv 67: 67: Test 67: 67: MarvinStereoGroupsZeros.mrv 67: 67: Test 67: 67: MarvinStereoGroupsAbs.mrv 67: 67: Test 67: 67: triphenylphosphine.mrv 67: 67: Test 67: 67: MarvinOldSuperGroupTest.mrv 67: 67: Test 67: 67: RadicalTests.mrv 67: 67: Test 67: 67: AnyBond.mrv 67: 67: Test 67: 67: cisBenzene.mrv 67: 67: Test 67: 67: DativeBond.mrv 67: 67: Test 67: 67: MultipleSgroup.mrv 67: 67: Test 67: 67: SgroupExpanded.mrv 67: 67: Test 67: 67: SgroupMultAttach.mrv 67: 67: Test 67: 67: MarvinMissingX2.mrv 67: 67: Test 67: 67: MarvinMissingY2.mrv 67: 67: Test 67: 67: DataSgroup.mrv 67: 67: Test 67: 67: MulticenterSgroup.mrv 67: 67: [09:08:14] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 67: [09:08:14] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 91: [09:08:14] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 67: Test 67: 67: GenericSgroup.mrv 67: 67: Test 67: 67: MonomerSgroup.mrv 67: 67: Test 67: 67: modification_sgroup.mrv 67: 67: Test 67: 67: copolymer_sgroup.mrv 67: 67: Test 67: 67: MultipleSgroupParentInMiddleOfAtomBlock.mrv 67: 67: Test 67: 67: EmbeddedSgroups.mrv 67: 67: Test 67: 67: marvin03.mrv 67: 67: Test 67: 67: MarvinBadMissingMolID.mrv 67: 67: [09:08:14] 67: 67: **** 67: Test Assert 67: Expression Failed: 67: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp 67: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr 67: ---------- 67: Stacktrace: 67: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 67: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 67: 2# 0x00005632600C099F in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 67: 3# 0x00005632600CB5EC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 67: 4# 0x00005632600B8A5D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 67: 5# 0x00007F6701231D68 in /lib/x86_64-linux-gnu/libc.so.6 67: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 67: 7# 0x00005632600B8BE1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 67: ---------- 67: **** 67: 67: Test 67: 67: MarvinBadMissingAtomID.mrv 67: 67: Expected id, elementType for an atom definition in MRV file 67: Test 67: 67: MarvinBadX2.mrv 67: 67: The values x2 and y2 must be large floats in MRV file 67: Test 67: 67: MarvinBadY2.mrv 67: 67: The values x2 and y2 must be large floats in MRV file 67: Test 67: 67: MarvinBadStereoGroupsAbs.mrv 67: 67: Unrecognized group definition 91: [09:08:14] product atom-mapping number 17 not found in reactants. 91: [09:08:14] product atom-mapping number 18 not found in reactants. 91: [09:08:14] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 12 67: Test 67: 67: MarvinBadElementType.mrv 67: 67: Test 67: 67: MarvinBadMissingBondID.mrv 67: 67: Test 67: 67: MarvinBadMissingBondAtomRefs 67: 67: Test 67: 67: MarvinBadMissingBondOrder.mrv 67: 67: bond must have one of: order, queryType, or convention in MRV File 67: Test 67: 67: MarvinBadMissingSruMolID.mrv 67: 67: Expected a molID in MRV file 67: Test 67: 67: MarvinBadMissingSruID.mrv 67: 67: Test 67: 67: MarvinBadMissingSruRole.mrv 67: 67: Test 67: 67: MarvinBadMissingSruAtomRef.mrv 67: 67: Test 67: 67: MarvinBadMissingSruTitle.mrv 67: 67: Test 67: 67: MarvinBadSruAtomRef.mrv 67: 67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 67: Test 67: 67: MarvinBadSruID.mrv 67: 67: Test 67: 67: MarvinBadSruRole.mrv 67: 67: Test 67: 67: MarvinBadSruAtomRef.mrv 67: 67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 67: Test 67: 67: MarvinBadSruAtomRef.mrv 67: 67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 67: Test 67: 67: MarvinBadSruConnect.mrv 67: 67: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file 67: Test 67: 67: MarvinBadSupAttachAtom.mrv 67: 67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 67: Test 67: 67: MarvinBadSupAttachBond.mrv 67: 67: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file 67: Test 67: 67: MarvinBadSupAttachOrder.mrv 67: 67: Order for an AttachmentPoint definition must be an integer in MRV file 67: Test 67: 67: MarvinBadSupAttachAtom.mrv 67: 67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 67: Test 67: 67: MarvinBadSupAttachAtom.mrv 67: 67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 67: Test 67: 67: MarvinBadSupAttachAtom.mrv 67: 67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 67: Test 67: 67: MarvinBadSupMissingAttachBond.mrv 67: 67: No attachment point found for bond to the condensed atom in a superatomSgroup 67: Test 67: 67: MarvinBadSupMissingAttachOrder.mrv 67: 67: Expected atom, order and bond, for an AttachmentPoint definition in MRV file 66: ..............[09:08:14] SMILES Parse Error: syntax error while parsing: invalidsmiles 66: [09:08:14] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' 88: done 88: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 88: processing2 88: launch2 :0 88: launch2 :1 88: launch2 :2 88: launch2 :3 88: done 88: preprocessing 3 88: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 88: processing3 88: launch3 :0 88: launch3 :1 88: launch3 :2 88: launch3 :3 94: Randomness seeded to: 3114013220 94: [09:08:14] atom 0 in product 0 has multiple charge specifications. 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 34 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 36 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 38 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 40 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 42 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 87 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 89 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 91 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 93 94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 95 67: Test 67: 67: marvin03.mrv 67: 67: Test 67: 67: Cubane.mrv 67: 67: Test 67: 67: FalseAtropisomer.mrv 67: 67: Test 67: 67: AtropEnhancedStereo.mrv 67: 67: Test 67: 67: AtropManyChirals.mrv 67: 67: Test 67: 67: AtropManyChiralsEnhanced.mrv 67: 67: Test 67: 67: AtropManyChiralsEnhanced2.mrv 67: 67: Test 67: 67: AtropManyChiralsEnhanced3.mrv 67: 67: Test 67: 67: AtropManyChiralsEnhanced4.mrv 67: 67: Test 67: 67: BMS-986142_3d_chiral.mrv 67: 67: Test 67: 67: BMS-986142_3d.mrv 67: 67: Test 67: 67: BMS-986142_atrop1.mrv 67: 67: Test 67: 67: BMS-986142_atrop2.mrv 67: 67: Test 67: 67: BMS-986142_atrop3.mrv 67: 67: Test 67: 67: BMS-986142_atrop4.mrv 67: 67: Test 67: 67: BMS-986142_atrop5.mrv 67: 67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 94: [09:08:14] mapped atoms in the reactants were not mapped in the products. 94: unmapped numbers are: 2 94: [09:08:14] mapped atoms in the reactants were not mapped in the products. 94: unmapped numbers are: 2 94: [09:08:14] SMARTS Parse Error: unclosed ring for input: 'CC1' 94: [09:08:14] SMILES Parse Error: unclosed ring for input: 'CC1' 91: [09:08:14] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 91: [09:08:14] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 91: 94: [09:08:14] mapped atoms in the reactants were not mapped in the products. 94: unmapped numbers are: 2 94: [09:08:14] product atom-mapping number 2 not found in reactants. 94: [09:08:14] mapped atoms in the reactants were not mapped in the products. 94: unmapped numbers are: 2 94: [09:08:14] product atom-mapping number 2 not found in reactants. 91: [09:08:14] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 91: ------------- 91: CCOc1ccccc1 67: Test 67: 67: BMS-986142_atrop6.mrv 67: 67: Test 67: 67: BMS-986142_atrop7.mrv 67: 67: Test 67: 67: BMS-986142_atrop8.mrv 67: 67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 94: [09:08:14] CX Extensions: Substance group hierarchy is not always preserved. 94: [09:08:14] CX Extensions: Substance group hierarchy is not always preserved. 67: Test 67: 67: BMS-986142_atropBad2.mrv 67: 67: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 93: 30000000 30000000 94: [09:08:14] reactant 0 has no mapped atoms. 94: [09:08:14] product 0 has no mapped atoms. 94: [09:08:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 94: [09:08:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 94: [09:08:14] Explicit valence for atom # 1 O, 5, is greater than permitted 67: Test 67: 67: JDQ443_3d.mrv 67: 67: Test 67: 67: JDQ443_atrop1.mrv 67: 67: Test 67: 67: JDQ443_atrop2.mrv 67: 67: Test 67: 67: JDQ443_atrop3.mrv 67: 67: Test 67: 67: JDQ443_atropBad1.mrv 67: 67: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 94: =============================================================================== 94: All tests passed (702 assertions in 28 test cases) 94: 75/230 Test #94: rxnTestCatch ........................... Passed 0.26 sec test 95 Start 95: pyChemReactions 95: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 95: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 95: Test timeout computed to be: 1500 67: Test 67: 67: RP-6306_atrop1.mrv 67: 67: Test 67: 67: RP-6306_atrop2.mrv 67: 67: Test 67: 67: RP-6306_atrop3.mrv 67: 67: Test 67: 67: RP-6306_atrop4.mrv 67: 67: Test 67: 67: RP-6306_atrop5.mrv 67: 67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: Test 67: 67: RP-6306_atropBad1.mrv 67: 67: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 67: Test 67: 67: RP-6306_atropBad2.mrv 67: 67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 68: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: [09:08:14] deprecated group abbreviation ignored on line 24 68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 68: [09:08:14] 68: 68: **** 68: Post-condition Violation 68: Element 'Mv' not found 68: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 68: Failed Expression: anum > -1 68: ---------- 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 3# 0x00007FE02B6C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 4# 0x00007FE02B6D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 5# 0x00007FE02B6D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 9# 0x0000556B52AD1CF5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 10# 0x0000556B52B384F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 11# 0x0000556B52AB8963 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 12# 0x00007FE02AC31D68 in /lib/x86_64-linux-gnu/libc.so.6 68: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 68: 14# 0x0000556B52AB8B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: ---------- 68: **** 68: 88: done 88: [09:08:14] done 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test GitHub issue 15 88: [09:08:14] done 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test GitHub issue 409 88: [09:08:14] done 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test chiral matching 88: [09:08:14] done 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test GitHub issue 688: partially specified chiral substructure queries don't work properly 88: [09:08:14] done 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test dative-bond matching 88: [09:08:14] done 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test cis/trans matching 88: [09:08:14] done 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test cis/trans matching part 2 88: [09:08:14] done 88: [09:08:14] ------------------------------------- 88: [09:08:14] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS 88: [09:08:14] done 89: Randomness seeded to: 3891049858 89: =============================================================================== 89: All tests passed (197 assertions in 9 test cases) 89: 88: [09:08:14] ------------------------------------- 88: [09:08:14] Testing matching E/Z against Cis/Trans stereo bonds 88: [09:08:14] 88: 88: **** 88: Pre-condition Violation 88: matches must not be empty 88: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 88: Failed Expression: !matches.empty() 88: ---------- 88: Stacktrace: 88: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 88: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 88: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 88: 4# 0x000055E860EFE536 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: 5# 0x000055E860EFBC21 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: 6# 0x00007F647A031D68 in /lib/x86_64-linux-gnu/libc.so.6 88: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 88: 8# 0x000055E860EFBD61 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: ---------- 88: **** 88: 88: [09:08:14] 88: 88: **** 88: Pre-condition Violation 88: matches must not be empty 88: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 88: Failed Expression: !matches.empty() 88: ---------- 88: Stacktrace: 88: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 88: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 88: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 88: 4# 0x000055E860EF1CF9 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: 5# 0x000055E860EFBC21 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: 6# 0x00007F647A031D68 in /lib/x86_64-linux-gnu/libc.so.6 88: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 88: 8# 0x000055E860EFBD61 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: ---------- 88: **** 88: 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test substructure matching with a pathological case for symmetric SSSR 76/230 Test #89: substructTestCatch ..................... Passed 0.58 sec test 96 Start 96: pyChemReactionEnumerations 96: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 96: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 96: Test timeout computed to be: 1500 88: [09:08:14] ------------------------------------- 88: [09:08:14] Test isAtomTerminalRGroupOrQueryHydrogen 66: ..... 66: ---------------------------------------------------------------------- 66: Ran 19 tests in 0.750s 66: 66: OK 77/230 Test #88: testSubstructMatch ..................... Passed 0.60 sec test 97 Start 97: pyChemReactionSanitize 97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 97: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 97: Test timeout computed to be: 1500 67: Test 67: 67: RP-6306_3d.mrv 67: 67: Test 67: 67: Sotorasib_atrop1.mrv 67: 67: Test 67: 67: Sotorasib_atrop2.mrv 67: 67: Test 67: 67: Sotorasib_atrop3.mrv 67: 67: Test 67: 67: Sotorasib_atrop4.mrv 67: 67: Test 67: 67: Sotorasib_atrop5.mrv 67: 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: Test 67: 67: Sotorasib_atropBad1.mrv 67: 67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 91: [09:08:15] reactant 0 has no mapped atoms. 91: [09:08:15] product 0 has no mapped atoms. 91: [09:08:15] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. 67: Test 67: 67: Sotorasib_atropBad2.mrv 67: 67: [09:08:15] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 78/230 Test #91: testReaction ........................... Passed 0.63 sec test 98 Start 98: testChemTransforms 98: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 98: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms 98: Test timeout computed to be: 1500 98: 1 smi: CC 98: 1 smi: CC 98: 2 smi: CCO[C@H](N)P 98: 2 smi: CC 98: replaceSub smi1:CCP(CC)[C@@H](N)O 98: replaceSub smi1:CCNCC 98: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 98: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O 98: [09:08:15] SMARTS Parse Error: syntax error while parsing: bar 98: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' 67: Test 67: 67: Sotorasib_3d.mrv 67: 67: Test 67: 67: ZM374979_atrop1.mrv 67: 67: Test 67: 67: ZM374979_atrop2.mrv 67: 67: Test 67: 67: ZM374979_atrop3.mrv 67: 67: Test 67: 67: ZM374979_atropBad1.mrv 67: 67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 68: [09:08:15] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 68: [09:08:15] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 79/230 Test #98: testChemTransforms ..................... Passed 0.11 sec test 99 Start 99: chemTransformsTestCatch 99: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms 99: Test timeout computed to be: 1500 67: Test 67: 67: mrtx1719_3d.mrv 67: 67: Test 67: 67: mrtx1719_atrop1.mrv 67: 67: Test 67: 67: mrtx1719_atrop2.mrv 67: 67: Test 67: 67: mrtx1719_atrop3.mrv 67: 67: Test 67: 67: mrtx1719_atropBad1.mrv 67: 67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 80/230 Test #66: pyDepictor ............................. Passed 1.59 sec test 100 Start 100: tautomerQueryTestCatch 100: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 100: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery 100: Test timeout computed to be: 1500 68: ---------------------------------- 68: ---------------------------------- 68: [09:08:15] 68: 68: **** 99: Randomness seeded to: 1545041524 99: [09:08:15] Incomplete atom labelling, cannot make bond 99: [09:08:15] 99: 99: **** 68: Pre-condition Violation 68: rlabel out of range for MDL files 68: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp 68: Failed Expression: rlabel >= 0 && rlabel < 100 68: ---------- 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 68: 3# 0x0000556B52ADF0FF in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 4# 0x0000556B52B3856A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 5# 0x0000556B52AB8963 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 6# 0x00007FE02AC31D68 in /lib/x86_64-linux-gnu/libc.so.6 68: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 68: 8# 0x0000556B52AB8B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: ---------- 68: **** 68: 68: [09:08:15] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 99: Invariant Violation 99: molzip: bond info already exists for end atom with label:1 99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 99: Failed Expression: !bond.b 99: ---------- 99: Stacktrace: 99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: 59: Test 59: 59: AtropCanon1.cxsmi 59: 59: Test 59: 59: AtropCanon2.cxsmi 59: 59: Test 59: 59: AtropCanon3.cxsmi 59: 59: Test 59: 59: BMS-986142_3d_chiral.cxsmi 59: 59: Test 59: 59: BMS-986142_3d.cxsmi 59: 59: =============================================================================== 59: All tests passed (2445 assertions in 29 test cases) 59: 99: [09:08:15] Incomplete atom labelling, cannot make bond 99: [09:08:15] 99: 99: **** 99: Invariant Violation 99: molzip: bond info already exists for end atom with label:1 99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 99: Failed Expression: !bond.b 99: ---------- 99: Stacktrace: 99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: 81/230 Test #59: cxsmilesTest ........................... Passed 1.76 sec test 101 Start 101: pyTautomerQuery 101: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 101: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 101: Test timeout computed to be: 1500 99: [09:08:15] Incomplete atom labelling, cannot make bond 99: [09:08:15] 99: 99: **** 99: Invariant Violation 99: molzip: bond info already exists for end atom with label:1 99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 99: Failed Expression: !bond.b 99: ---------- 99: Stacktrace: 99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: 99: [09:08:15] Incomplete atom labelling, cannot make bond 99: [09:08:15] Incomplete atom labelling, cannot make bond 99: [09:08:15] Incomplete atom labelling, cannot make bond 99: [09:08:15] 99: 99: **** 99: Invariant Violation 99: molzip: bond info already exists for end atom with label:1 99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 99: Failed Expression: !bond.b 99: ---------- 99: Stacktrace: 99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: 99: [09:08:15] Incomplete atom labelling, cannot make bond 99: [09:08:15] 99: 99: **** 99: Invariant Violation 99: molzip: bond info already exists for end atom with label:1 99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 99: Failed Expression: !bond.b 99: ---------- 99: Stacktrace: 99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: 99: [09:08:15] 99: 99: **** 99: Invariant Violation 99: molzip: zipped Bond already exists, perhaps labels are duplicated 99: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 99: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) 99: ---------- 99: Stacktrace: 99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 5# 0x000055E87A3E243D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 6# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 7# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 8# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 9# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 10# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 11# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: 12# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 99: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 99: 14# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: 99: =============================================================================== 99: All tests passed (674 assertions in 9 test cases) 99: 82/230 Test #99: chemTransformsTestCatch ................ Passed 0.14 sec test 102 Start 102: testSubgraphs1 102: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 102: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 102: Test timeout computed to be: 1500 102: ----------------------- 102: Subgraph retrieval 102: Finished 102: ----------------------- 102: testSubgraphs2a 102: Finished 102: ----------------------- 102: testSubgraphs2 67: Test 67: 67: FalseAtropisomer.mrv 67: 67: Test 67: 67: AtropEnhancedStereo.mrv 67: 67: Test 67: 67: AtropManyChirals.mrv 67: 67: Test 67: 67: AtropManyChiralsEnhanced.mrv 67: 67: Test 67: 67: AtropManyChiralsEnhanced2.mrv 67: 67: Test 67: 67: AtropManyChiralsEnhanced3.mrv 67: 67: Test 67: 67: AtropManyChiralsEnhanced4.mrv 67: 67: Test 67: 67: BMS-986142_3d_chiral.mrv 67: 67: Test 67: 67: BMS-986142_3d.mrv 67: 67: Test 67: 67: BMS-986142_atrop1.mrv 67: 67: Test 67: 67: BMS-986142_atrop2.mrv 67: 67: Test 67: 67: BMS-986142_atrop3.mrv 67: 67: Test 67: 67: BMS-986142_atrop4.mrv 67: 67: Test 67: 67: BMS-986142_atrop5.mrv 67: 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 102: Finished 102: ----------------------- 102: Path retrieval 102: Finished 102: ----------------------- 102: Path retrieval2 102: Finished 102: ----------------------- 102: Unique Subgraph retrieval 102: Finished 102: ----------------------- 102: testUniqueSubgraphs2 95: ...[09:08:15] 95: 95: **** 67: Test 67: 67: BMS-986142_atrop6.mrv 67: 67: Test 67: 67: BMS-986142_atrop7.mrv 67: 67: Test 67: 67: BMS-986142_atrop8.mrv 67: 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 95: Pre-condition Violation 95: getNumImplicitHs() called without preceding call to calcImplicitValence() 95: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp 95: Failed Expression: d_implicitValence > -1 95: ---------- 95: Stacktrace: 95: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 95: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 95: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 95: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 95: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 95: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 95: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 95: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 25# 0x00007FA463A4B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 95: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 95: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 95: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 95: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 95: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 95: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 36# 0x00007FA460FAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 37# 0x00007FA460FAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 38# 0x00007FA460FAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 39# 0x00007FA460FAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 40# 0x00007FA460FAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 95: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 95: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 95: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 95: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 46# 0x00007FA463A483C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 47# _PyObject_MakeTpCall in /usr/bin/python3 95: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 49# 0x0000000000546E76 in /usr/bin/python3 95: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 51# _PyObject_Call_Prepend in /usr/bin/python3 95: 52# 0x000000000059D6E4 in /usr/bin/python3 95: 53# _PyObject_MakeTpCall in /usr/bin/python3 95: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 55# 0x0000000000546E76 in /usr/bin/python3 95: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 57# _PyObject_Call_Prepend in /usr/bin/python3 95: 58# 0x000000000059D6E4 in /usr/bin/python3 95: 59# _PyObject_MakeTpCall in /usr/bin/python3 95: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 61# 0x0000000000546E76 in /usr/bin/python3 95: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 63# _PyObject_Call_Prepend in /usr/bin/python3 95: 64# 0x000000000059D6E4 in /usr/bin/python3 95: 65# _PyObject_MakeTpCall in /usr/bin/python3 95: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 67# _PyObject_Call_Prepend in /usr/bin/python3 95: 68# 0x000000000059810D in /usr/bin/python3 95: 69# 0x0000000000593E22 in /usr/bin/python3 95: 70# _PyObject_MakeTpCall in /usr/bin/python3 95: 71# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 72# PyEval_EvalCode in /usr/bin/python3 95: 73# 0x00000000005FFE7F in /usr/bin/python3 95: 74# 0x00000000006A59F2 in /usr/bin/python3 95: 75# _PyRun_SimpleFileObject in /usr/bin/python3 95: 76# _PyRun_AnyFileObject in /usr/bin/python3 95: 77# Py_RunMain in /usr/bin/python3 95: 78# Py_BytesMain in /usr/bin/python3 95: 79# 0x00007FA464391D68 in /lib/x86_64-linux-gnu/libc.so.6 95: 80# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 95: 81# _start in /usr/bin/python3 95: ---------- 95: **** 95: 95: [09:08:15] 95: 95: **** 67: Test 67: 67: BMS-986142_atropBad2.mrv 67: 67: [09:08:15] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 95: Pre-condition Violation 95: getNumImplicitHs() called without preceding call to calcImplicitValence() 95: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp 95: Failed Expression: d_implicitValence > -1 95: ---------- 95: Stacktrace: 95: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 95: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 95: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 95: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 95: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 95: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 95: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 95: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 95: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 95: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 25# 0x00007FA463A4B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 95: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 95: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 95: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 95: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 95: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 95: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 36# 0x00007FA460FAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 37# 0x00007FA460FAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 38# 0x00007FA460FAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 39# 0x00007FA460FAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 40# 0x00007FA460FAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 95: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 95: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 95: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 95: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 46# 0x00007FA463A483C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 47# _PyObject_MakeTpCall in /usr/bin/python3 95: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 49# 0x0000000000546E76 in /usr/bin/python3 95: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 51# _PyObject_Call_Prepend in /usr/bin/python3 95: 52# 0x000000000059D6E4 in /usr/bin/python3 95: 53# _PyObject_MakeTpCall in /usr/bin/python3 95: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 55# 0x0000000000546E76 in /usr/bin/python3 95: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 57# _PyObject_Call_Prepend in /usr/bin/python3 95: 58# 0x000000000059D6E4 in /usr/bin/python3 95: 59# _PyObject_MakeTpCall in /usr/bin/python3 95: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 61# 0x0000000000546E76 in /usr/bin/python3 95: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 63# _PyObject_Call_Prepend in /usr/bin/python3 95: 64# 0x000000000059D6E4 in /usr/bin/python3 95: 65# _PyObject_MakeTpCall in /usr/bin/python3 95: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 67# _PyObject_Call_Prepend in /usr/bin/python3 95: 68# 0x000000000059810D in /usr/bin/python3 95: 69# 0x0000000000593E22 in /usr/bin/python3 95: 70# _PyObject_MakeTpCall in /usr/bin/python3 95: 71# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 72# PyEval_EvalCode in /usr/bin/python3 95: 73# 0x00000000005FFE7F in /usr/bin/python3 95: 74# 0x00000000006A59F2 in /usr/bin/python3 95: 75# _PyRun_SimpleFileObject in /usr/bin/python3 95: 76# _PyRun_AnyFileObject in /usr/bin/python3 95: 77# Py_RunMain in /usr/bin/python3 95: 78# Py_BytesMain in /usr/bin/python3 95: 79# 0x00007FA464391D68 in /lib/x86_64-linux-gnu/libc.so.6 95: 80# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 95: 81# _start in /usr/bin/python3 95: ---------- 95: **** 95: 90: Randomness seeded to: 1813137230 90: =============================================================================== 90: All tests passed (11480 assertions in 38 test cases) 90: 83/230 Test #90: testGenericGroups ...................... Passed 1.07 sec test 103 Start 103: testSubgraphs2 103: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 103: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 103: Test timeout computed to be: 1500 95: .........[09:08:15] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 95: [09:08:15] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 95: [09:08:15] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 95: [09:08:15] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 95: .[09:08:15] product atom-mapping number 1 found multiple times. 95: [09:08:15] product atom-mapping number 1 found multiple times. 100: Randomness seeded to: 1851626409 100: =============================================================================== 100: All tests passed (93 assertions in 13 test cases) 100: 84/230 Test #100: tautomerQueryTestCatch ................. Passed 0.29 sec test 104 Start 104: subgraphsCatch 104: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 104: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 104: Test timeout computed to be: 1500 95: ................[09:08:15] mapped atoms in the reactants were not mapped in the products. 95: unmapped numbers are: 3 95: [09:08:15] mapped atoms in the reactants were not mapped in the products. 95: unmapped numbers are: 3 67: Test 67: 67: JDQ443_3d.mrv 67: 67: Test 67: 67: JDQ443_atrop1.mrv 67: 67: Test 67: 67: JDQ443_atrop2.mrv 67: 67: Test 67: 67: JDQ443_atrop3.mrv 67: 67: Test 67: 67: JDQ443_atropBad1.mrv 67: 67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 97: .[09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 103: ----------------------- 103: Test1: pathToSubmol 97: .[09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 95: .[09:08:15] mapped atoms in the reactants were not mapped in the products. 95: unmapped numbers are: 3 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: () 97: ******************************************** 97: $RXN 97: 97: RDKit 97: 97: 2 1 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 1 0 0 0 0 0 0999 V2000 97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 1 2 1 0 97: M RGP 1 2 1 97: V 1 halogen.bromine.aromatic 97: V 2 [*:1] 97: M STY 1 1 DAT 97: M SAL 1 1 1 97: M SED 1 [#35&$([Br&$(Br-&!@c)])] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 4 3 0 1 0 0 0 0 0 0999 V2000 97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 2 3 1 0 97: 1 2 1 0 97: 2 4 1 0 97: M RGP 1 1 2 97: V 1 [*:2] 97: V 2 boronicacid 97: M STY 1 1 DAT 97: M SAL 1 1 2 97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 0 0 0 0 0 0 0999 V2000 97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 97: 1 2 1 0 97: M RGP 2 1 1 2 2 97: V 1 [*:1] 97: V 2 [*:2] 97: M END 97: 97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 97: $RXN 97: 97: RDKit 97: 97: 2 1 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 1 0 0 0 0 0 0999 V2000 97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 1 2 1 0 97: M RGP 1 2 1 97: V 1 halogen.bromine.aromatic 97: V 2 [*:1] 97: M STY 1 1 DAT 97: M SAL 1 1 1 97: M SED 1 [#35&$([Br&$(Br-&!@c)])] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 4 3 0 1 0 0 0 0 0 0999 V2000 97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 2 3 1 0 97: 1 2 1 0 97: 2 4 1 0 97: M RGP 1 1 2 97: V 1 [*:2] 97: V 2 boronicacid 97: M STY 1 1 DAT 97: M SAL 1 1 2 97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 0 0 0 0 0 0 0999 V2000 97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 97: 1 2 1 0 97: M RGP 2 1 1 2 2 97: V 1 [*:1] 97: V 2 [*:2] 97: M END 97: 97: ******************************************** 97: $RXN 97: 97: RDKit 97: 97: 2 1 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 1 0 0 0 0 0 0999 V2000 97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 97: 1 2 1 0 97: M RGP 1 2 1 97: V 1 halogen.bromine.aromatic 97: V 2 * 97: M STY 1 1 DAT 97: M SAL 1 1 1 97: M SED 1 [#35&$([Br&$(Br-&!@c)])] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 4 3 0 1 0 0 0 0 0 0999 V2000 97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 2 3 1 0 97: 1 2 1 0 97: 2 4 1 0 97: M RGP 1 1 2 97: V 1 * 97: V 2 boronicacid 97: M STY 1 1 DAT 97: M SAL 1 1 2 97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 0 0 0 0 0 0 0999 V2000 97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 97: 1 2 1 0 97: M RGP 2 1 1 2 2 97: V 1 * 97: V 2 * 97: M END 97: 97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 97: $RXN 97: 97: RDKit 97: 97: 2 1 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 1 0 0 0 0 0 0999 V2000 97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 1 2 1 0 97: M RGP 1 2 1 97: V 1 halogen.bromine.aromatic 97: V 2 [*:1] 97: M STY 1 1 DAT 97: M SAL 1 1 1 97: M SED 1 [#35&$([Br&$(Br-&!@c)])] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 4 3 0 1 0 0 0 0 0 0999 V2000 97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 2 3 1 0 97: 1 2 1 0 97: 2 4 1 0 97: M RGP 1 1 2 97: V 1 [*:2] 97: V 2 boronicacid 97: M STY 1 1 DAT 97: M SAL 1 1 2 97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 0 0 0 0 0 0 0999 V2000 97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 97: 1 2 1 0 97: M RGP 2 1 1 2 2 97: V 1 [*:1] 97: V 2 [*:2] 97: M END 97: 97: ******************************************** 97: $RXN 97: 97: RDKit 97: 97: 2 1 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 1 0 0 0 0 0 0999 V2000 97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 97: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 97: 1 2 1 0 97: M ISO 1 2 1 97: V 1 halogen.bromine.aromatic 97: M STY 1 1 DAT 97: M SAL 1 1 1 97: M SED 1 [#35&$([Br&$(Br-&!@c)])] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 4 3 0 1 0 0 0 0 0 0999 V2000 97: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 2 3 1 0 97: 1 2 1 0 97: 2 4 1 0 97: M ISO 1 1 2 97: V 2 boronicacid 97: M STY 1 1 DAT 97: M SAL 1 1 2 97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 0 0 0 0 0 0 0999 V2000 97: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 97: 1 2 1 0 97: M ISO 2 1 1 2 2 97: M END 97: 97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 97: $RXN 97: 97: RDKit 97: 97: 2 1 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 1 0 0 0 0 0 0999 V2000 97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 1 2 1 0 97: M RGP 1 2 1 97: V 1 halogen.bromine.aromatic 97: V 2 [*:1] 97: M STY 1 1 DAT 97: M SAL 1 1 1 97: M SED 1 [#35&$([Br&$(Br-&!@c)])] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 4 3 0 1 0 0 0 0 0 0999 V2000 97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 2 3 1 0 97: 1 2 1 0 97: 2 4 1 0 97: M RGP 1 1 2 97: V 1 [*:2] 97: V 2 boronicacid 97: M STY 1 1 DAT 97: M SAL 1 1 2 97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 0 0 0 0 0 0 0999 V2000 97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 97: 1 2 1 0 97: M RGP 2 1 1 2 2 97: V 1 [*:1] 97: V 2 [*:2] 97: M END 97: 97: ******************************************** 97: $RXN 97: 97: RDKit 97: 97: 2 1 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 1 0 0 0 0 0 0999 V2000 97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 97: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 97: 1 2 1 0 97: M ISO 1 2 1 97: V 1 halogen.bromine.aromatic 97: M STY 1 1 DAT 97: M SAL 1 1 1 97: M SED 1 [#35&$([Br&$(Br-&!@c)])] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 4 3 0 1 0 0 0 0 0 0999 V2000 97: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 2 3 1 0 97: 1 2 1 0 97: 2 4 1 0 97: M ISO 1 1 3 97: V 2 boronicacid 97: M STY 1 1 DAT 97: M SAL 1 1 2 97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 0 0 0 0 0 0 0999 V2000 97: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 97: 1 2 1 0 97: M ISO 2 1 1 2 2 97: M END 97: [09:08:15] reactant 0 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] product 0 has no mapped atoms. 97: [09:08:15] Could not find RLabel mapping for atom: 0 in template: 1 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 97: [09:08:15] reactant 1 has no mapped atoms. 67: Test 67: 67: RP-6306_atrop1.mrv 67: 67: Test 67: 67: RP-6306_atrop2.mrv 67: 67: Test 67: 67: RP-6306_atrop3.mrv 67: 67: Test 67: 67: RP-6306_atrop4.mrv 67: 67: Test 67: 67: RP-6306_atrop5.mrv 67: 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 97: .. 97: ---------------------------------------------------------------------- 97: Ran 4 tests in 0.028s 97: 97: OK 97: 97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 97: $RXN 97: 97: RDKit 97: 97: 2 1 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 1 0 0 0 0 0 0999 V2000 97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 1 2 1 0 97: M RGP 1 2 1 97: V 1 halogen.bromine.aromatic 97: V 2 [*:1] 97: M STY 1 1 DAT 97: M SAL 1 1 1 97: M SED 1 [#35&$([Br&$(Br-&!@c)])] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 4 3 0 1 0 0 0 0 0 0999 V2000 97: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 97: 2 3 1 0 97: 1 2 1 0 97: 2 4 1 0 97: M ISO 1 1 3 97: V 2 boronicacid 97: M STY 1 1 DAT 97: M SAL 1 1 2 97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 97: M END 97: $MOL 97: 97: RDKit 2D 97: 97: 2 1 0 0 0 0 0 0 0 0999 V2000 97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 97: 1 2 1 0 97: M ISO 1 2 2 97: M RGP 1 1 1 97: V 1 [*:1] 97: M END 97: 97: $RXN Failed 67: Test 67: 67: RP-6306_atropBad1.mrv 67: 67: [09:08:15] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 95: ..[09:08:15] reactant 2 has no mapped atoms. 95: [09:08:15] reactant 2 has no mapped atoms. 95: [09:08:15] product 1 has no mapped atoms. 67: Test 67: 67: RP-6306_atropBad2.mrv 67: 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 96: [09:08:15] == testCartesianProduct 95: ........[09:08:15] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q 95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' 95: [09:08:15] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q 95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' 95: .[09:08:15] reactant atom-mapping number 1 found multiple times. 95: [09:08:15] product atom-mapping number 2 not found in reactants. 95: [09:08:15] mapped atoms in the reactants were not mapped in the products. 95: unmapped numbers are: 4 95: [09:08:15] product atom-mapping number 5 not found in reactants. 103: Finished 103: ----------------------- 103: Test2: Atom Environments 103: Finished 103: ----------------------- 103: Test 3: Atom Environments (Extension) 103: Finished 103: ----------------------- 103: Testing github Issue103: stereochemistry and pathToSubmol 104: Randomness seeded to: 3263048636 104: --------- 104: =============================================================================== 104: All tests passed (11 assertions in 1 test case) 104: 103: Finished 103: ----------------------- 103: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 103: Finished 96: .[09:08:15] == testEnumerateLibrary 85/230 Test #103: testSubgraphs2 ......................... Passed 0.08 sec 86/230 Test #104: subgraphsCatch ......................... Passed 0.06 sec test 105 Start 105: filterCatalogTest 105: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 105: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog 105: Test timeout computed to be: 1500 test 106 Start 106: pyFilterCatalog 106: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 106: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 106: Test timeout computed to be: 1500 96: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> 96: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) 96: ResourceWarning: Enable tracemalloc to get the object allocation traceback 67: Test 67: 67: RP-6306_3d.mrv 67: 67: Test 67: 67: Sotorasib_atrop1.mrv 67: 67: Test 67: 67: Sotorasib_atrop2.mrv 67: 67: Test 67: 67: Sotorasib_atrop3.mrv 67: 67: Test 67: 67: Sotorasib_atrop4.mrv 67: 67: Test 67: 67: Sotorasib_atrop5.mrv 67: 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: Test 67: 67: Sotorasib_atropBad1.mrv 67: 67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 67: Test 67: 67: Sotorasib_atropBad2.mrv 67: 67: [09:08:15] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 95: ........./build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> 95: png = open(fname, 'rb').read() 95: ResourceWarning: Enable tracemalloc to get the object allocation traceback 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 34 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 36 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 38 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 40 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 42 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 87 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 89 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 91 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 93 95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 95 67: Test 67: 67: Sotorasib_3d.mrv 67: 67: Test 67: 67: ZM374979_atrop1.mrv 67: 67: Test 67: 67: ZM374979_atrop2.mrv 67: 67: Test 67: 67: ZM374979_atrop3.mrv 67: 67: Test 67: 67: ZM374979_atropBad1.mrv 67: 67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 95: ..[09:08:15] SMARTS Parse Error: syntax error while parsing: boromicacid 95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 95: [09:08:15] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 95: [09:08:15] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 96: ..[09:08:15] == testRGroupState 87/230 Test #97: pyChemReactionSanitize ................. Passed 0.65 sec test 107 Start 107: testFragCatalog 107: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog 107: Test timeout computed to be: 1500 95: [09:08:15] reaction has no reactants 95: [09:08:15] reaction has no products 95: [09:08:15] initialization failed 95: [09:08:15] reaction has no reactants 95: [09:08:15] reaction has no products 95: .[09:08:15] SMARTS Parse Error: syntax error while parsing: boromicacid 95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 96: .[09:08:15] == testRandomEnumerateAllBBsLibrary 96: ** [1, 1] 96: ** [0, 2] 96: ** [1, 0] 95: [09:08:15] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 102: Finished 102: ----------------------- 102: testRootedSubgraphs 102: Finished 102: ----------------------- 102: testRootedPaths 102: Finished 95: [09:08:15] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 95: [09:08:15] reaction has no reactants 95: [09:08:15] reaction has no products 95: [09:08:15] initialization failed 95: [09:08:15] reaction has no reactants 95: [09:08:15] reaction has no products 95: . 95: ---------------------------------------------------------------------- 95: Ran 54 tests in 0.240s 95: 95: OK 88/230 Test #102: testSubgraphs1 ......................... Passed 0.34 sec test 108 Start 108: pyFragCatalog 108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 108: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 108: Test timeout computed to be: 1500 95: ******************************************** 95: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/AmideBond.rxn 95: 67: Test 67: 67: mrtx1719_3d.mrv 67: 67: Test 67: 67: mrtx1719_atrop1.mrv 67: 67: Test 67: 67: mrtx1719_atrop2.mrv 67: 67: Test 67: 67: mrtx1719_atrop3.mrv 67: 67: Test 67: 67: mrtx1719_atropBad1.mrv 67: 67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 96: .[09:08:15] == testRandomEnumerateLibrary 107: 21 68: [09:08:15] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 68: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 96: .[09:08:15] == testRandomSample 96: .[09:08:15] == testRandomSampleAllBBs 67: Test 67: 67: AlexRxn.mrv 67: 67: Test 67: 67: BadReactionSign.mrv 67: 67: Test 67: 67: bondArray_node.mrv 67: 67: Test 67: 67: marvin03.mrv 67: 67: Test 67: 67: marvin04.mrv 67: 67: Test 67: 67: marvin08.mrv 67: 67: Test 67: 67: marvin09.mrv 67: 67: Test 67: 67: marvin11.mrv 67: 67: Test 67: 67: marvin05.mrv 67: 67: Test 67: 67: EmptyRxn.mrv 67: 67: [09:08:15] initialization failed 96: .[09:08:15] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 96: [09:08:15] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 96: .[09:08:15] == testRemoveBadMatches 96: .[09:08:15] == testTimings 105: Warning: molecule failed filter 105: Warning: molecule failed filter: reason hzone_phenol_A(479) 105: v = { 105: 0,23}, 105: 1,22}, 105: 2,20}, 105: 3,19}, 105: 4,25}, 105: 5,24}, 105: 6,18}, 105: 7,17}, 105: 8,16}, 105: 9,21}, 105: } 105: match = { 105: 0,23}, 105: 1,22}, 105: 2,20}, 105: 3,19}, 105: 4,25}, 105: 5,24}, 105: 6,18}, 105: 7,17}, 105: 8,16}, 105: 9,21}, 105: } 105: Warning: molecule failed filter 105: Warning: molecule failed filter: reason cyano_imine_B(17) 105: v = { 105: 0,11}, 105: 1,12}, 105: 2,13}, 105: 3,14}, 105: 4,15}, 105: 5,10}, 105: 6,9}, 105: 7,8}, 105: 8,7}, 105: 9,6}, 105: 10,5}, 105: 11,17}, 105: 12,16}, 105: } 105: match = { 105: 0,11}, 105: 1,12}, 105: 2,13}, 105: 3,14}, 105: 4,15}, 105: 5,10}, 105: 6,9}, 105: 7,8}, 105: 8,7}, 105: 9,6}, 105: 10,5}, 105: 11,17}, 105: 12,16}, 105: } 105: Warning: molecule failed filter 105: Warning: molecule failed filter: reason keto_keto_gamma(5) 105: v = { 105: 0,0}, 105: 1,1}, 105: 2,2}, 105: 3,4}, 105: 4,5}, 105: 5,6}, 105: 6,7}, 105: 7,8}, 105: 8,9}, 105: 9,14}, 105: 10,15}, 105: 11,16}, 105: } 105: match = { 105: 0,0}, 105: 1,1}, 105: 2,2}, 105: 3,4}, 105: 4,5}, 105: 5,6}, 105: 6,7}, 105: 7,8}, 105: 8,9}, 105: 9,14}, 105: 10,15}, 105: 11,16}, 105: } 67: Test 67: 67: RxnNoCoords.mrv 67: 67: Test 67: 67: mrvValenceZero.mrv 67: 67: Test 67: 67: condition_coordinates_mpoint.mrv 67: 67: Test 67: 67: marvin01.mrv 67: 67: Test 67: 67: aspirineSynthesisWithAttributes.mrv 67: 67: Test 67: 67: marvin01.mrv 67: 67: Test 67: 67: NewChiralTest 67: 67: Test 67: 67: NewChiralTest 67: 67: Test 67: 67: NewChiralTestNoChiral 67: 67: Test 67: 67: NewChiralTestNoChiral 67: 67: Test 67: 67: NewChiralTest2 67: 67: Test 67: 67: NewChiralTest2 67: 67: Test 67: 67: NewChiralTest2AllChiral 67: 67: Test 67: 67: NewChiralTest2AllChiral 67: 67: Test 67: 67: Vendor839 67: 67: Test 67: 67: DoubleBondChain 67: 67: Test 67: 67: Na_Mg_Al_OH 67: 67: Test 67: 67: Pb 67: 67: Test 67: 67: O_Mg_Si 67: 67: Test 67: 67: SquiggleBond 67: 67: Test 67: 67: BigMacrocycle 67: 67: Test 67: 67: Smiles1 67: 89/230 Test #67: testMrvToMol ........................... Passed 2.13 sec test 109 Start 109: testDescriptors 109: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 109: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 109: Test timeout computed to be: 1500 90/230 Test #95: pyChemReactions ........................ Passed 0.90 sec test 110 Start 110: testAUTOCORR2D 110: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 110: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 110: Test timeout computed to be: 1500 101: ..... 101: ---------------------------------------------------------------------- 101: Ran 5 tests in 0.043s 101: 101: OK 109: [09:08:15] ------------------------------------- 109: [09:08:15] Test Crippen parameter acquisition. 109: [09:08:15] done 109: [09:08:15] ------------------------------------- 109: [09:08:15] Test Crippen calculation. 68: [09:08:15] Empty atom list: 'M ALS 1 0 F' on line 8. 68: de_DE.UTF-8 68: [09:08:15] ------------------------------------- 68: [09:08:15] Test multithreading Locale Switching 110: [09:08:15] ---------------------------- 110: start test autocorr2D 109: [09:08:15] done 109: [09:08:15] ------------------------------------- 109: [09:08:15] Test Issue262: problems with Crippen calculation from pickles. 109: [09:08:15] done 109: [09:08:15] ------------------------------------- 109: [09:08:15] Test AMW calculation. 109: [09:08:15] done 109: [09:08:15] ------------------------------------- 109: [09:08:15] Test Exact MW calculation. 109: [09:08:15] done 109: [09:08:15] ------------------------------------- 109: [09:08:15] Test Labute ASA descriptors. 109: [09:08:15] done 109: [09:08:15] ------------------------------------- 109: [09:08:15] Test TPSA descriptors. 91/230 Test #101: pyTautomerQuery ........................ Passed 0.62 sec test 111 Start 111: testATF 111: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF 111: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 109: [09:08:15] done 109: [09:08:15] ------------------------------------- 109: [09:08:15] Test Lipinski parameters. 92/230 Test #111: testATF ................................ Passed 0.04 sec test 112 Start 112: testBCUT 112: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 112: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 112: [09:08:15] ------------------------------------- 112: [09:08:15] Basic BCUT tests. 68: [09:08:15] Test multithreading (Done) 68: [09:08:15] ------------------------------------- 112: [09:08:15] done 112: [09:08:15] ------------------------------------- 112: [09:08:15] Larger BCUT tests. 68: *************************************** 68: *************************************** 68: [09:08:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: [09:08:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: [09:08:16] bond with order 0 found on line 7. This is not part of the MDL specification. 109: [09:08:16] done 109: [09:08:16] ------------------------------------- 109: [09:08:16] Test VSA descriptors. 109: [09:08:16] done 109: [09:08:16] ------------------------------------- 109: [09:08:16] Test molecular formula calculation. 109: [09:08:16] done 109: [09:08:16] ------------------------------------- 109: [09:08:16] Test Issue 3415534. 109: [09:08:16] done 109: [09:08:16] ------------------------------------- 109: [09:08:16] Test Issue3433771: Bad definition for Crippen atom type O11. 109: [09:08:16] done 109: [09:08:16] ------------------------------------- 109: [09:08:16] Test multithreading 109: reading molecules 68: [09:08:16] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 68: [09:08:16] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 68: [09:08:16] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 93/230 Test #105: filterCatalogTest ...................... Passed 0.52 sec test 113 Start 113: testEEM 113: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM 113: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 109: processing 109: launch :0 109: launch :1 109: launch :2 109: launch :3 68: generating smiles 68: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 68: converting back 68: check isomorphism 113: =>start test EEM 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: 0 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 110: [09:08:16] done 110: [09:08:16] ------------------------------------- 110: [09:08:16] Test Github #3806: NaNs from AUTOCORR2D descriptor 110: [09:08:16] done 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 94/230 Test #110: testAUTOCORR2D ......................... Passed 0.66 sec test 114 Start 114: testPBF 114: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF 114: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 114: Test timeout computed to be: 1500 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: 100 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: ......... 108: ---------------------------------------------------------------------- 108: Ran 9 tests in 0.107s 108: 108: OK 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 114: [09:08:16] ------------------------------------- 114: [09:08:16] Basic PBF tests. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 112: [09:08:16] ------------------------------------- 112: [09:08:16] Test empty molecule BCUT. 95/230 Test #112: testBCUT ............................... Passed 0.63 sec test 115 Start 115: testRDFcustom 115: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 115: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 115: Test timeout computed to be: 1500 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 96/230 Test #108: pyFragCatalog .......................... Passed 1.02 sec test 116 Start 116: testRDF 116: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF 116: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 116: Test timeout computed to be: 1500 39: [09:08:16] done: 500000 39: [09:08:16] Done 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: 200 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 39: [09:08:16] Testing hanoi with a functor. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 39: [09:08:16] Done 39: [09:08:16] Testing basic partition refinement. 39: [09:08:16] Done 39: [09:08:16] Testing partition refinement with neighbors. 39: [09:08:16] Done 39: [09:08:16] testing canonicalization via tie breaking. 39: [09:08:16] Done 39: [09:08:16] testing canonicalization using the wrapper. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 39: [09:08:16] Done 39: [09:08:16] testing some specific ordering problems 39: [09:08:16] Finished 39: [09:08:16] testing chiral invariants. 39: [09:08:16] Finished 39: [09:08:16] testing unique ranks in w.r.t. renumbering. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 39: [09:08:16] Finished 39: [09:08:16] testing mol fragments. 39: [09:08:16] Finished 39: [09:08:16] testing protein round-tripping. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 87: Randomness seeded to: 2322531019 87: [09:08:16] Explicit valence for atom # 9 N, 6, is greater than permitted 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: 300 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 114: [09:08:17] done 114: [09:08:17] ------------------------------------- 114: [09:08:17] PBF edge cases. 114: [09:08:17] done 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 97/230 Test #114: testPBF ................................ Passed 0.69 sec test 117 Start 117: testMORSE 117: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 117: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 117: Test timeout computed to be: 1500 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: 400 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107: [09:08:17] 107: 107: **** 107: Invariant Violation 107: nonsense 107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 107: Failed Expression: token != tokens.end() 107: ---------- 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 2# 0x00007F2F2883EEFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 4# 0x000055B3F0B2B183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: 5# 0x000055B3F0B28731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: 6# 0x00007F2F27A31D68 in /lib/x86_64-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 107: 8# 0x000055B3F0B28861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: 107: [09:08:17] 107: 107: **** 107: Invariant Violation 107: nonsense no new line 107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 107: Failed Expression: token != tokens.end() 107: ---------- 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 2# 0x00007F2F2883EEFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 4# 0x000055B3F0B2B183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: 5# 0x000055B3F0B28731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: 6# 0x00007F2F27A31D68 in /lib/x86_64-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 107: 8# 0x000055B3F0B28861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: 107: [09:08:17] 107: 107: **** 107: Invariant Violation 107: nonsense with tab 107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 107: Failed Expression: token != tokens.end() 107: ---------- 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 2# 0x00007F2F2883EEFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 4# 0x000055B3F0B2B183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: 5# 0x000055B3F0B28731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: 6# 0x00007F2F27A31D68 in /lib/x86_64-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 107: 8# 0x000055B3F0B28861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 98/230 Test #107: testFragCatalog ........................ Passed 1.60 sec test 118 Start 118: test3D 118: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D 118: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 118: Test timeout computed to be: 1500 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 118: [09:08:17] ------------------------------------- 118: [09:08:17] Basic PMI tests. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: Elapsed time: 1.21878 s 113: Errors:0 113: [09:08:17] test on : 500 molecules done 99/230 Test #113: testEEM ................................ Passed 1.27 sec test 119 Start 119: testWHIM 119: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 119: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 119: Test timeout computed to be: 1500 68: [09:08:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: [09:08:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: [09:08:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: [09:08:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: [09:08:17] deprecated group abbreviation ignored on line 24 68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 68: [09:08:17] 68: 68: **** 68: Post-condition Violation 68: Element 'Mv' not found 68: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 68: Failed Expression: anum > -1 68: ---------- 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 3# 0x00007FE02B6C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 4# 0x00007FE02B6D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 5# 0x00007FE02B6D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 9# 0x0000556B52AD1CF5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 10# 0x0000556B52B384F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 11# 0x0000556B52AB89E3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 12# 0x00007FE02AC31D68 in /lib/x86_64-linux-gnu/libc.so.6 68: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 68: 14# 0x0000556B52AB8B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: ---------- 68: **** 68: 118: [09:08:17] done 118: [09:08:17] ------------------------------------- 118: [09:08:17] More PMI/NPR tests. 118: [09:08:17] done 118: [09:08:17] ------------------------------------- 118: [09:08:17] Basic NPR tests. 106: .............[09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 106: [09:08:17] dasfsadf 87: [09:08:17] Explicit valence for atom # 3 Al, 6, is greater than permitted 39: [09:08:17] Finished 39: [09:08:17] testing stability w.r.t. renumbering. 106: .[09:08:17] SMILES Parse Error: syntax error while parsing: mydoghasfleas 106: [09:08:17] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' 39: [09:08:17] Finished 39: [09:08:17] testing smiles round-tripping. 118: [09:08:17] done 118: [09:08:17] ------------------------------------- 118: [09:08:17] PMI edge cases. 118: [09:08:17] done 118: [09:08:17] ------------------------------------- 118: [09:08:17] NPR edge cases. 118: [09:08:17] done 118: [09:08:17] ------------------------------------- 118: [09:08:17] 3D descriptors. 118: [09:08:17] done 118: [09:08:17] ------------------------------------- 118: [09:08:17] 3D descriptor edge cases. 118: [09:08:17] done 118: [09:08:17] ------------------------------------- 118: [09:08:17] Inertial shape factor. 118: [09:08:17] done 100/230 Test #118: test3D ................................. Passed 0.59 sec test 120 Start 120: testGETAWAY 120: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 120: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 68: [09:08:17] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 68: [09:08:17] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 87: [09:08:17] Explicit valence for atom # 4 Al, 6, is greater than permitted 96: . 96: ---------------------------------------------------------------------- 96: Ran 11 tests in 2.387s 96: 96: OK 96: True 96: == CartesianProductStrategy CartesianProductStrategy 96: 197 out of 300 96: 0 6 out of 10 96: 1 3 out of 5 96: 2 4 out of 6 96: 198 out of 300 96: 0 10 out of 10 96: 1 5 out of 5 96: 2 6 out of 6 96: Skipped 10000000 in 0.14346098899841309 seconds 96: Skipped 10000000 in 1.4000003337860107 seconds 96: Skipped 10000000 in 0.31561708450317383 seconds 39: [09:08:17] Finished 39: [09:08:17] testing github #1567: Non-canonical result from MolFragmentToSmiles() 39: [09:08:17] Finished 101/230 Test #39: hanoiTest .............................. Passed 4.91 sec test 121 Start 121: testAUTOCORR3D 121: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 121: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 87: [09:08:18] Explicit valence for atom # 10 Si, 6, is greater than permitted 68: ---------------------------------- 68: ---------------------------------- 68: [09:08:18] 68: 68: **** 68: Pre-condition Violation 68: rlabel out of range for MDL files 68: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp 68: Failed Expression: rlabel >= 0 && rlabel < 100 68: ---------- 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 68: 3# 0x0000556B52ADF0FF in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 4# 0x0000556B52B3856A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 5# 0x0000556B52AB89E3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: 6# 0x00007FE02AC31D68 in /lib/x86_64-linux-gnu/libc.so.6 68: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 68: 8# 0x0000556B52AB8B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: ---------- 68: **** 68: 68: [09:08:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 106: ....... 106: ---------------------------------------------------------------------- 106: Ran 21 tests in 2.022s 106: 106: OK 106: (Five aromatic carbons And (Not any of Five aromatic carbons)) 106: (Five aromatic carbons Or (Not any of Five aromatic carbons)) 106: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) 106: ******************************************** 106: Testing: PAINS_A 2 106: ******************************************** 106: Testing: PAINS_B 4 106: ******************************************** 106: Testing: PAINS_C 8 106: ******************************************** 106: Testing: PAINS 14 106: (Not FilterMatcher) 106: Bar 106: Count 1 106: ******************************************** 106: {'Cl,Br,I'} 106: 1 106: 2 106: running 102/230 Test #96: pyChemReactionEnumerations ............. Passed 3.15 sec test 122 Start 122: testCoulombMat 122: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 122: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 122: ===================== Testing CoulombMat ======================= 122: CM test 1 mat Done 103/230 Test #122: testCoulombMat ......................... Passed 0.05 sec test 123 Start 123: descriptorsTestCatch 123: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 123: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 123: Randomness seeded to: 3502967058 123: Warning: Atom Count for residue GLU5A does not match expected count 123: Warning: Atom Count for residue ASN39A does not match expected count 123: Warning: Atom Count for residue GLU53A does not match expected count 123: Warning: Atom Count for residue ARG64A does not match expected count 123: Warning: Atom Count for residue LYS80A does not match expected count 104/230 Test #106: pyFilterCatalog ........................ Passed 2.71 sec test 124 Start 124: pyMolDescriptors 124: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 124: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap 124: Test timeout computed to be: 1500 123: Warning: Atom Count for residue GLU150A does not match expected count 123: Warning: Atom Count for residue ASN157A does not match expected count 119: =>start test WHIM 119: [09:08:18] test on : 365 molecules done 105/230 Test #119: testWHIM ............................... Passed 0.95 sec test 125 Start 125: pyMolDescriptors3D 125: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Wrap/test3D.py" 125: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap 125: Test timeout computed to be: 1500 27: All 191 tests passed 123: Warning: Atom Count for residue GLU5A does not match expected count 116: =>start test rdf 116: [09:08:18] test on : 365 molecules done 106/230 Test #116: testRDF ................................ Passed 1.84 sec test 126 Start 126: testFingerprints 126: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 126: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 126: Test timeout computed to be: 1500 27: 27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: Atoms: 126: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: 1 conj?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: a conj?: 1 aromatic?: 1 126: 7 7->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: 1 conj?: 1 126: 9 8->10 order: a conj?: 1 aromatic?: 1 126: 10 10->1 order: a conj?: 1 aromatic?: 1 126: 11 7->3 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: SMI: Oc1cc2[nH]cnc2c(O)n1 126: Atoms: 126: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: 1 conj?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: a conj?: 1 aromatic?: 1 126: 7 7->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: 1 conj?: 1 126: 9 8->10 order: a conj?: 1 aromatic?: 1 126: 10 10->1 order: a conj?: 1 aromatic?: 1 126: 11 7->3 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: c1(O)cc2[nH]cnc2c(O)n1 126: Atoms: 126: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: 1 conj?: 1 126: 1 0->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: a conj?: 1 aromatic?: 1 126: 7 7->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: 1 conj?: 1 126: 9 8->10 order: a conj?: 1 aromatic?: 1 126: 10 10->0 order: a conj?: 1 aromatic?: 1 126: 11 7->3 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: c1c(O)nc(O)c2c1[nH]cn2 126: Atoms: 126: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: a conj?: 1 aromatic?: 1 126: 1 1->2 order: 1 conj?: 1 126: 2 1->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: 1 conj?: 1 126: 5 4->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: a conj?: 1 aromatic?: 1 126: 7 7->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: a conj?: 1 aromatic?: 1 126: 9 9->10 order: a conj?: 1 aromatic?: 1 126: 10 7->0 order: a conj?: 1 aromatic?: 1 126: 11 10->6 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: c12cc(O)nc(O)c1nc[nH]2 126: Atoms: 126: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: a conj?: 1 aromatic?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: 1 conj?: 1 126: 3 2->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: 1 conj?: 1 126: 6 5->7 order: a conj?: 1 aromatic?: 1 126: 7 7->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: a conj?: 1 aromatic?: 1 126: 9 9->10 order: a conj?: 1 aromatic?: 1 126: 10 7->0 order: a conj?: 1 aromatic?: 1 126: 11 10->0 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: [nH]1c2cc(O)nc(O)c2nc1 126: Atoms: 126: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: a conj?: 1 aromatic?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: 1 conj?: 1 126: 4 3->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: 1 conj?: 1 126: 7 6->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: a conj?: 1 aromatic?: 1 126: 9 9->10 order: a conj?: 1 aromatic?: 1 126: 10 10->0 order: a conj?: 1 aromatic?: 1 126: 11 8->1 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: c1[nH]c2cc(O)nc(O)c2n1 126: Atoms: 126: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: a conj?: 1 aromatic?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: 1 conj?: 1 126: 5 4->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: a conj?: 1 aromatic?: 1 126: 7 7->8 order: 1 conj?: 1 126: 8 7->9 order: a conj?: 1 aromatic?: 1 126: 9 9->10 order: a conj?: 1 aromatic?: 1 126: 10 10->0 order: a conj?: 1 aromatic?: 1 126: 11 9->2 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: n1c[nH]c2cc(O)nc(O)c21 126: Atoms: 126: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: a conj?: 1 aromatic?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: 1 conj?: 1 126: 6 5->7 order: a conj?: 1 aromatic?: 1 126: 7 7->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: 1 conj?: 1 126: 9 8->10 order: a conj?: 1 aromatic?: 1 126: 10 10->0 order: a conj?: 1 aromatic?: 1 126: 11 10->3 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: c12c(cc(O)nc1O)[nH]cn2 126: Atoms: 126: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: a conj?: 1 aromatic?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: 1 conj?: 1 126: 4 3->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: 1 conj?: 1 126: 7 1->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: a conj?: 1 aromatic?: 1 126: 9 9->10 order: a conj?: 1 aromatic?: 1 126: 10 6->0 order: a conj?: 1 aromatic?: 1 126: 11 10->0 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 126: Atoms: 126: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: 1 conj?: 1 126: 1 0->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: 1 conj?: 1 126: 6 5->7 order: a conj?: 1 aromatic?: 1 126: 7 3->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: a conj?: 1 aromatic?: 1 126: 9 9->10 order: a conj?: 1 aromatic?: 1 126: 10 7->0 order: a conj?: 1 aromatic?: 1 126: 11 10->2 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: Oc1c2c(cc(O)n1)[nH]cn2 126: Atoms: 126: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: Bonds: 126: 0 0->1 order: 1 conj?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: 1 conj?: 1 126: 6 5->7 order: a conj?: 1 aromatic?: 1 126: 7 3->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: a conj?: 1 aromatic?: 1 126: 9 9->10 order: a conj?: 1 aromatic?: 1 126: 10 7->1 order: a conj?: 1 aromatic?: 1 126: 11 10->2 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: SMI: n1c(O)cc2[nH]cnc2c1O 126: Atoms: 126: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: Bonds: 126: 0 0->1 order: a conj?: 1 aromatic?: 1 126: 1 1->2 order: 1 conj?: 1 126: 2 1->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: a conj?: 1 aromatic?: 1 126: 7 7->8 order: a conj?: 1 aromatic?: 1 126: 8 8->9 order: a conj?: 1 aromatic?: 1 126: 9 9->10 order: 1 conj?: 1 126: 10 9->0 order: a conj?: 1 aromatic?: 1 126: 11 8->4 order: a conj?: 1 aromatic?: 1 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 126: 126: 126: 126: 126: 126: 126: 126: 126: ------------------- 126: 68: [09:08:18] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 68: [09:08:18] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Morgan Fingerprints. 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Morgan Fingerprints using fromAtoms argument. 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Morgan Fingerprints as bit vects. 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Morgan Fingerprints with feature invariants. 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test additional Morgan fingerprints options. 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Atom Codes. 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Atom Pairs. 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Atom Pairs part 2. 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Topological Torsions. 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Bulk Topological Torsions. 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 115: =>start test rdf custom 115: [09:08:18] test on : 365 molecules done 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 121: =>start test autocorr3D 121: [09:08:18] test on : 365 molecules done 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 107/230 Test #121: testAUTOCORR3D ......................... Passed 0.78 sec test 127 Start 127: testMHFPFingerprint 127: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 127: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 127: Test timeout computed to be: 1500 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 127: [09:08:18] ------------------------------------- 127: [09:08:18] Test MHFP fingerprint encoder initialization 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: [09:08:18] Empty atom list: 'M ALS 1 0 F' on line 8. 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 108/230 Test #68: fileParsersTest1 ....................... Passed 5.19 sec test 128 Start 128: testFingerprintGenerators 128: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 128: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 128: Test timeout computed to be: 1500 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 127: [09:08:18] done 127: [09:08:18] ------------------------------------- 127: [09:08:18] Test MHFP shingling creation 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: ..[09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: .[09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: ..[09:08:18] 124: 124: **** 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: Pre-condition Violation 124: Number of atom props not equal to number of atoms 124: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp 124: Failed Expression: atom_props.size() == num_atoms 124: ---------- 124: Stacktrace: 124: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 124: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 124: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 124: 3# 0x00007F90CECA25D2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 124: 4# 0x00007F90CECB2256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 124: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 124: 6# 0x00007F90D330B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 124: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 124: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 124: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 124: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 124: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 124: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 124: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 124: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 124: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 124: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 124: 17# 0x00007F90D09AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 124: 18# 0x00007F90D09AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 124: 19# 0x00007F90D09AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 124: 20# 0x00007F90D09AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 124: 21# 0x00007F90D09AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 124: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 124: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 124: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 124: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 124: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 124: 27# 0x00007F90D33083C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 124: 28# _PyObject_MakeTpCall in /usr/bin/python3 124: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 124: 30# 0x0000000000546E76 in /usr/bin/python3 124: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 124: 32# _PyObject_Call_Prepend in /usr/bin/python3 124: 33# 0x000000000059D6E4 in /usr/bin/python3 124: 34# _PyObject_MakeTpCall in /usr/bin/python3 124: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 124: 36# 0x0000000000546E76 in /usr/bin/python3 124: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 124: 38# _PyObject_Call_Prepend in /usr/bin/python3 124: 39# 0x000000000059D6E4 in /usr/bin/python3 124: 40# _PyObject_MakeTpCall in /usr/bin/python3 124: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 124: 42# 0x0000000000546E76 in /usr/bin/python3 124: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 124: 44# _PyObject_Call_Prepend in /usr/bin/python3 124: 45# 0x000000000059D6E4 in /usr/bin/python3 124: 46# _PyObject_MakeTpCall in /usr/bin/python3 124: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 124: 48# _PyObject_Call_Prepend in /usr/bin/python3 124: 49# 0x000000000059810D in /usr/bin/python3 124: 50# 0x0000000000593E22 in /usr/bin/python3 124: 51# _PyObject_MakeTpCall in /usr/bin/python3 124: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 124: 53# PyEval_EvalCode in /usr/bin/python3 124: 54# 0x00000000005FFE7F in /usr/bin/python3 124: 55# 0x00000000006A59F2 in /usr/bin/python3 124: 56# _PyRun_SimpleFileObject in /usr/bin/python3 124: 57# _PyRun_AnyFileObject in /usr/bin/python3 124: 58# Py_RunMain in /usr/bin/python3 124: 59# Py_BytesMain in /usr/bin/python3 124: 60# 0x00007F90D3AE1D68 in /lib/x86_64-linux-gnu/libc.so.6 124: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 124: 62# _start in /usr/bin/python3 124: ---------- 124: **** 124: 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test atom-pair fp generator 127: [09:08:18] done 127: [09:08:18] ------------------------------------- 127: [09:08:18] Test MHFP hashing of string and uint arrays 127: [09:08:18] done 127: [09:08:18] ------------------------------------- 127: [09:08:18] Test SECFP fingerprint functionality 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test atom-pair fp generator with different arguments 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 124: ...Warning: Atom Count for residue GLU5A does not match expected count 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 127: [09:08:18] done 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: Warning: Atom Count for residue ASN39A does not match expected count 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test atom-pair additional output 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test Folded Atom Pairs. 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test Rooted Atom Pairs. 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test ignoring atoms in Atom Pairs. 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test Atom Pairs including info about chirality. 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test Morgan Fingerprints. 124: Warning: Atom Count for residue GLU53A does not match expected count 109/230 Test #127: testMHFPFingerprint .................... Passed 0.15 sec test 129 Start 129: fpTestCatch 129: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 129: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 124: Warning: Atom Count for residue ARG64A does not match expected count 124: Warning: Atom Count for residue LYS80A does not match expected count 124: Warning: Atom Count for residue GLU150A does not match expected count 124: Warning: Atom Count for residue ASN157A does not match expected count 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test morgan fp generator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test Morgan Fingerprints using fromAtoms argument. 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test Morgan Fingerprints as bit vects. 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test Morgan Fingerprints with feature invariants. 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test additional Morgan fingerprints options. 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Single atoms setting radius 1 bits in Morgan fingerprints 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test different invariant generator combinations 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test invariant overriding 128: [09:08:18] done 128: [09:08:18] ------------------------------------- 128: [09:08:18] Test RDKit fp generator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 87: [09:08:18] Explicit valence for atom # 2 O, 4, is greater than permitted 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Hashed Atom Pairs. 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Hashed torsions. 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Rooted Atom Pairs. 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test ignoring atoms in Atom Pairs. 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test Rooted Topological Torsions. 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test ignoring atoms in Topological Torsions. 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test atom info from morgan fingerprints. 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] Test atom info from morgan fingerprints including Info Redundant Environments. 126: [09:08:18] done 126: [09:08:18] ------------------------------------- 126: [09:08:18] ------------------------------------- 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:18] ------------------------------------- 129: Randomness seeded to: 3789818418 129: =============================================================================== 129: All tests passed (188 assertions in 16 test cases) 129: 110/230 Test #129: fpTestCatch ............................ Passed 0.09 sec test 130 Start 130: fpGenTestCatch 130: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 130: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 126: [09:08:19] ------------------------------------- 126: [09:08:19] ------------------------------------- 126: [09:08:19] ------------------------------------- 126: [09:08:19] Test Atom Pairs including info about chirality. 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] done 126: [09:08:19] ------------------------------------- 126: [09:08:19] Test Topological Torsions including info about chirality. 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] done 126: [09:08:19] ------------------------------------- 126: [09:08:19] Test GitHub Issue 25: fingerprint backwards compatibility. 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] done 126: [09:08:19] ------------------------------------- 126: [09:08:19] Test GitHub Issue 151: PatternFingerprint problems 87: [09:08:19] Explicit valence for atom # 3 Al, 6, is greater than permitted 87: [09:08:19] Explicit valence for atom # 3 Be, 4, is greater than permitted 126: [09:08:19] done 126: [09:08:19] ------------------------------------- 126: [09:08:19] Test 3D atom pairs. 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:19] done 126: [09:08:19] ------------------------------------- 126: [09:08:19] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule 126: [09:08:19] done 126: [09:08:19] ------------------------------------- 126: [09:08:19] Test multithreading with the pattern FP 126: reading molecules 124: Warning: Atom Count for residue GLU5A does not match expected count 12: .................. 12: ---------------------------------------------------------------------- 12: Ran 18 tests in 5.973s 12: 12: OK 126: pass 1 126: launch :0 126: launch :1 126: launch :2 126: launch :3 111/230 Test #41: resMolSupplierTest ..................... Passed 6.04 sec test 131 Start 131: pyTestGenerator 131: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 131: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 131: Test timeout computed to be: 1500 87: [09:08:19] Explicit valence for atom # 27 P, 6, is greater than permitted 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test unfolded version of RDKFP 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test topological torsion fp generator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 112/230 Test #12: pyBV ................................... Passed 6.53 sec test 132 Start 132: pyTestMHFP 132: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 132: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 132: Test timeout computed to be: 1500 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test Topological Torsions. 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test Folded torsions. 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test Bulk Topological Torsions. 130: Randomness seeded to: 1044882225 130: =============================================================================== 130: All tests passed (2692 assertions in 5 test cases) 130: 113/230 Test #130: fpGenTestCatch ......................... Passed 0.41 sec test 133 Start 133: testPartialCharges 133: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 133: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges 133: Test timeout computed to be: 1500 123: Warning: Atom Count for residue ASN39A does not match expected count 117: =>start test MORSE 117: =>read file 117: [09:08:19] test on : 365 molecules done 114/230 Test #133: testPartialCharges ..................... Passed 0.07 sec test 134 Start 134: pyPartialCharges 134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 134: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 134: Test timeout computed to be: 1500 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test Rooted Topological Torsions. 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test ignoring atoms in Topological Torsions. 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test Topological Torsions including info about chirality. 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test GitHub Issue 25: fingerprint backwards compatibility. 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test convenience and bulk fp calculation functions 115/230 Test #117: testMORSE .............................. Passed 2.38 sec test 135 Start 135: testMolTransforms 135: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 135: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 135: Test timeout computed to be: 1500 126: pass 2 126: launch :0 126: launch :1 126: launch :2 126: launch :3 135: *********************************************************** 135: Testing MolTransforms 135: --------------------------------- 135: test1Canonicalization 135: 135: --------------------------------- 135: testGetSetBondLength 135: 135: --------------------------------- 135: testGetSetAngle 135: 135: --------------------------------- 135: testGetSetDihedral 135: 135: --------------------------------- 135: testGetSetDihedralThroughTripleBond 135: 135: --------------------------------- 135: testGithub1262: PMI descriptors incorrect 135: 135: --------------------------------- 135: testGithub1908: CanonicalizeMol() distorting bond lengths 135: 135: --------------------------------- 135: testGithub4302: native computeCanonicalTransform() generates non-canonical coords 135: 135: --------------------------------- 135: testWeightedCentroid 135: 135: *********************************************************** 116/230 Test #135: testMolTransforms ...................... Passed 0.08 sec test 136 Start 136: molTransformsTestCatch 136: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch 136: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 136: Test timeout computed to be: 1500 136: Randomness seeded to: 698560435 136: =============================================================================== 136: All tests passed (4 assertions in 1 test case) 136: 117/230 Test #136: molTransformsTestCatch ................. Passed 0.08 sec test 137 Start 137: pyMolTransforms 137: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 137: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 137: Test timeout computed to be: 1500 125: ........ 125: ---------------------------------------------------------------------- 125: Ran 8 tests in 0.490s 125: 125: OK 123: Warning: Atom Count for residue GLU53A does not match expected count 131: .............. 131: ---------------------------------------------------------------------- 131: Ran 14 tests in 0.259s 131: 131: OK 128: [09:08:19] done 128: [09:08:19] ------------------------------------- 128: [09:08:19] Test GitHub Issue #6958 128: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator 118/230 Test #128: testFingerprintGenerators .............. Passed 1.14 sec test 138 Start 138: forceFieldHelpersCatch 138: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 138: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers 138: Test timeout computed to be: 1500 123: Warning: Atom Count for residue ARG64A does not match expected count 138: Randomness seeded to: 2573869229 138: =============================================================================== 138: All tests passed (11 assertions in 1 test case) 138: 119/230 Test #138: forceFieldHelpersCatch ................. Passed 0.06 sec test 139 Start 139: testMMFFForceFieldHelpers 139: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 139: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 139: Test timeout computed to be: 1500 120/230 Test #131: pyTestGenerator ........................ Passed 0.91 sec test 140 Start 140: testMMFFForceFieldHelpersMultiThread 140: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 140: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 140: Test timeout computed to be: 1500 139: [09:08:20] ------------------------------------- 139: [09:08:20] Test MMFF atom types. 115: =>start test morse custom 115: [09:08:20] test on : 365 molecules done 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing MMFF builder tools. 140: [09:08:20] ------------------------------------- 140: [09:08:20] Test MMFF multithreading 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing MMFF builder+minimization. 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing Issue239. 134: ....... 134: ---------------------------------------------------------------------- 134: Ran 7 tests in 0.163s 134: 134: OK 124: Warning: Atom Count for residue ASN39A does not match expected count 121/230 Test #125: pyMolDescriptors3D ..................... Passed 1.95 sec test 141 Start 141: testUFFForceFieldHelpers 141: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 141: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 141: Test timeout computed to be: 1500 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing calcEnergy with passed coords. 140: processing 140: launch :0 140: launch :1 140: launch :2 140: launch :3 140: launch :4 140: launch :5 140: launch :6 140: launch :7 140: launch :8 140: launch :9 140: launch :10 140: launch :11 140: launch :12 140: launch :13 140: launch :14 140: launch :15 140: launch :16 140: launch :17 140: launch :18 140: launch :19 140: launch :20 140: launch :21 140: launch :22 140: launch :23 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing calcGrad. 141: [09:08:20] ------------------------------------- 141: [09:08:20] Test UFF atom labels. 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Test UFF atom typer. 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing UFF builder tools. 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing UFF builder+minimization. 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing Issue242. 122/230 Test #134: pyPartialCharges ....................... Passed 0.89 sec test 142 Start 142: testCrystalForceField 142: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 142: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 142: Test timeout computed to be: 1500 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing github 308: crash during MMFF parameterization . 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing SFIssue1653802. 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Testing SFIssue2378119. 139: [09:08:20] done 139: [09:08:20] ------------------------------------- 139: [09:08:20] Test MMFF force-field parameter getters. 139: [09:08:20] ------------------------------------- 139: [09:08:20] Test MMFF multithreading 139: generating reference data 142: ------------------------------------- 142: Test CrystalFF torsional term. 115: =>start test AUTOCORR3D custom 115: [09:08:20] test on : 365 molecules done 123: Warning: Atom Count for residue LYS80A does not match expected count 132: .. 132: ---------------------------------------------------------------------- 132: Ran 2 tests in 0.070s 132: 132: OK 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing UFF special cases. 141: [09:08:20] UFFTYPER: Unrecognized charge state for atom: 0 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing Issue239. 124: Warning: Atom Count for residue GLU53A does not match expected count 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing calcEnergy with passed coords. 123/230 Test #132: pyTestMHFP ............................. Passed 1.39 sec test 143 Start 143: pyForceFieldHelpers 143: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 143: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 143: Test timeout computed to be: 1500 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing calcGrad. 115: =>start test 2 WHIM custom 115: [09:08:20] test on : 365 molecules done 124/230 Test #142: testCrystalForceField .................. Passed 0.41 sec test 144 Start 144: testDistGeomHelpers 144: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 144: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 144: Test timeout computed to be: 1500 137: ........ 137: ---------------------------------------------------------------------- 137: Ran 8 tests in 0.095s 137: 137: OK 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing SFIssue1653802. 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing SFIssue2378119. 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Test UFF force-field parameter getters. 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing handling missing parameters. 141: [09:08:20] UFFTYPER: Unrecognized hybridization for atom: 0 141: [09:08:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) 141: [09:08:20] UFFTYPER: Unrecognized hybridization for atom: 0 141: [09:08:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) 144: [09:08:20] ******************************************************** 144: [09:08:20] Testing DistGeomHelpers 144: [09:08:20] --------------------------------- 144: [09:08:20] test2 144: 144: go 144: ------------------------------------- 144: 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Testing SFIssue3009337. 141: [09:08:20] done 141: [09:08:20] ------------------------------------- 141: [09:08:20] Test UFF multithreading 140: done 140: [09:08:20] done 141: generating reference data 124: Warning: Atom Count for residue ARG64A does not match expected count 115: =>start test 1 WHIM custom 115: [09:08:21] test on : 365 molecules done 125/230 Test #140: testMMFFForceFieldHelpersMultiThread ... Passed 0.97 sec test 145 Start 145: distGeomHelpersCatch 145: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 145: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 145: Test timeout computed to be: 1500 126/230 Test #137: pyMolTransforms ........................ Passed 1.39 sec test 146 Start 146: pyDistGeomHelpers 146: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 146: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 146: Test timeout computed to be: 1500 145: Randomness seeded to: 1882134578 139: processing 139: launch :0 139: launch :1 139: launch :2 139: launch :3 139: [09:08:21] Rep: 0 Mol:1 139: [09:08:21] Rep: 0 Mol:0 139: [09:08:21] Rep: 0 Mol:3 139: [09:08:21] Rep: 0 Mol:5 145: [09:08:21] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] 139: [09:08:21] Rep: 0 Mol:2 139: [09:08:21] Rep: 0 Mol:9 145: [09:08:21] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] 139: [09:08:21] Rep: 0 Mol:4 139: [09:08:21] Rep: 0 Mol:13 145: [09:08:21] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 139: [09:08:21] Rep: 0 Mol:17 145: [09:08:21] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: ----------- 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 145: ----------- 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 139: [09:08:21] Rep: 0 Mol:8 139: [09:08:21] Rep: 0 Mol:6 145: [09:08:21] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 145: ----------- 139: [09:08:21] Rep: 0 Mol:12 139: [09:08:21] Rep: 0 Mol:10 145: ----------- 139: [09:08:21] Rep: 0 Mol:21 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 145: [09:08:21] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 139: [09:08:21] Rep: 0 Mol:25 139: [09:08:21] Rep: 0 Mol:16 139: [09:08:21] Rep: 0 Mol:29 139: [09:08:21] Rep: 0 Mol:7 139: [09:08:21] Rep: 0 Mol:11 139: [09:08:21] Rep: 0 Mol:15 139: [09:08:21] Rep: 0 Mol:20 139: [09:08:21] Rep: 0 Mol:19 139: [09:08:21] Rep: 0 Mol:23 139: [09:08:21] Rep: 0 Mol:27 139: [09:08:21] Rep: 0 Mol:31 139: [09:08:21] Rep: 0 Mol:24 139: [09:08:21] Rep: 0 Mol:28 139: [09:08:21] Rep: 0 Mol:14 139: [09:08:21] Rep: 0 Mol:18 139: [09:08:21] Rep: 0 Mol:22 139: [09:08:21] Rep: 0 Mol:26 145: [09:08:21] UFFTYPER: Unrecognized atom type: Pt5+2 (1) 139: [09:08:21] Rep: 0 Mol:30 145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 1 145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 1 124: Warning: Atom Count for residue LYS80A does not match expected count 145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 1 139: [09:08:21] Rep: 20 Mol:1 139: [09:08:21] Rep: 20 Mol:5 139: [09:08:21] Rep: 20 Mol:9 139: [09:08:21] Rep: 20 Mol:13 139: [09:08:21] Rep: 20 Mol:17 139: [09:08:21] Rep: 20 Mol:21 139: [09:08:21] Rep: 20 Mol:25 139: [09:08:21] Rep: 20 Mol:29 143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:21] Rep: 20 Mol:2 139: [09:08:21] Rep: 20 Mol:6 139: [09:08:21] Rep: 20 Mol:10 141: processing 141: launch :0 141: launch :1 141: launch :2 141: launch :3 141: [09:08:21] Rep: 0 Mol:2 139: [09:08:21] Rep: 20 Mol:14 139: [09:08:21] Rep: 20 Mol:18 139: [09:08:21] Rep: 20 Mol:22 139: [09:08:21] Rep: 20 Mol:26 139: [09:08:21] Rep: 20 Mol:30 143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:21] Rep: 0 Mol:1 141: [09:08:21] Rep: 0 Mol:0 141: [09:08:21] Rep: 0 Mol:3 143: ..[09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 143: .[09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 141: [09:08:21] Rep: 0 Mol:5 143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:21] Rep: 0 Mol:9 141: [09:08:21] Rep: 0 Mol:4 120: =>start test GETAWAY 120: [09:08:21] test on : 365 molecules done 141: [09:08:21] Rep: 0 Mol:6 141: [09:08:21] Rep: 0 Mol:13 127/230 Test #120: testGETAWAY ............................ Passed 4.11 sec test 147 Start 147: testMolAlign 147: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 147: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 147: Test timeout computed to be: 1500 141: [09:08:21] Rep: 0 Mol:10 141: [09:08:21] Rep: 0 Mol:7 141: [09:08:21] Rep: 0 Mol:11 141: [09:08:21] Rep: 0 Mol:8 141: [09:08:21] Rep: 0 Mol:15 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test Issue252: Bad definitions for Crippen atom types. 141: [09:08:21] Rep: 0 Mol:17 143: .[09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:21] Rep: 0 Mol:12 141: [09:08:21] Rep: 0 Mol:16 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test calculation of ChiVs. 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test calculation of ChiNs. 141: [09:08:21] Rep: 0 Mol:19 141: [09:08:21] Rep: 0 Mol:23 141: [09:08:21] Rep: 0 Mol:27 141: [09:08:21] Rep: 0 Mol:20 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test calculation of HallKierAlpha. 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test calculation of Kappa1. 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 141: [09:08:21] Rep: 0 Mol:24 141: [09:08:21] Rep: 0 Mol:31 109: [09:08:21] Test calculation of Kappa2. 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test calculation of Kappa3. 141: [09:08:21] Rep: 0 Mol:28 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test Crippen atom type calculations. 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test ring descriptors 145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 5 141: [09:08:21] Rep: 0 Mol:14 139: [09:08:21] Rep: 20 Mol:3 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test other count descriptors. 109: [09:08:21] done 109: [09:08:21] ------------------------------------- 109: [09:08:21] Test MQN 145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 5 141: [09:08:22] Rep: 0 Mol:18 139: [09:08:22] Rep: 20 Mol:7 139: [09:08:22] Rep: 20 Mol:11 139: [09:08:22] Rep: 20 Mol:15 139: [09:08:22] Rep: 20 Mol:19 139: [09:08:22] Rep: 20 Mol:23 139: [09:08:22] Rep: 20 Mol:27 139: [09:08:22] Rep: 20 Mol:31 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test GitHub Issue 56. 109: [09:08:22] WARNING: not removing hydrogen atom without neighbors 109: [09:08:22] WARNING: not removing hydrogen atom without neighbors 109: [09:08:22] WARNING: not removing hydrogen atom without neighbors 109: [09:08:22] WARNING: not removing hydrogen atom without neighbors 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test Github92: Bad Crippen atom type for pyrrole H. 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test Github362: order dependence in Kier-Hall descriptors. 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test calculation of spiro and bridgehead counts. 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test Github694: ExactMolWt ignoring the mass of the electron 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Testing Properties and KitchenSink 141: [09:08:22] Rep: 0 Mol:21 109: [09:08:22] ---Caught keyerror (bad property name)--- 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test USR Descriptor 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test Github #1973: support P and S terms for TPSA calculation 141: [09:08:22] Rep: 0 Mol:22 109: [09:08:22] done 109: [09:08:22] ------------------------------------- 109: [09:08:22] Test Github #2948: Empty molecule has non-zero LabuteASA 109: [09:08:22] done 128/230 Test #109: testDescriptors ........................ Passed 6.27 sec test 148 Start 148: testO3AAlign 148: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 148: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 148: Test timeout computed to be: 1500 141: [09:08:22] Rep: 0 Mol:26 141: [09:08:22] Rep: 0 Mol:25 145: [09:08:22] UFFTYPER: Unrecognized charge state for atom: 5 146: .[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:22] Rep: 0 Mol:30 141: [09:08:22] Rep: 0 Mol:29 139: [09:08:22] Rep: 20 Mol:0 139: [09:08:22] Rep: 20 Mol:4 139: [09:08:22] Rep: 20 Mol:8 143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 20 Mol:12 139: [09:08:22] Rep: 20 Mol:16 139: [09:08:22] Rep: 20 Mol:20 139: [09:08:22] Rep: 20 Mol:24 139: [09:08:22] Rep: 20 Mol:28 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 123: Warning: Atom Count for residue GLU150A does not match expected count 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: ..[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:1 139: [09:08:22] Rep: 40 Mol:5 139: [09:08:22] Rep: 40 Mol:9 145: [09:08:22] UFFTYPER: Unrecognized charge state for atom: 6 87: [09:08:22] Explicit valence for atom # 9 N, 6, is greater than permitted 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:13 139: [09:08:22] Rep: 40 Mol:17 139: [09:08:22] Rep: 40 Mol:21 139: [09:08:22] Rep: 40 Mol:25 139: [09:08:22] Rep: 40 Mol:29 146: ..[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:08:22] UFFTYPER: Unrecognized charge state for atom: 6 146: .[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: .[09:08:22] UFFTYPER: Unrecognized hybridization for atom: 0 143: [09:08:22] UFFTYPER: Unrecognized atom type: Cu+1 (0) 143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 147: *********************************************************** 147: Testing MolAlign 147: --------------------------------- 147: test1MolAlign 147: 147: --------------------------------- 147: test1GetBestRMS 147: 147: --------------------------------- 147: test1MolWithQueryAlign 147: 147: --------------------------------- 147: test2AtomMap 147: 147: --------------------------------- 147: test3Weights 147: 147: --------------------------------- 147: testIssue241 147: 147: *********************************************************** 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: .[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: ...[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 145: [09:08:22] UFFTYPER: Unrecognized charge state for atom: 6 129/230 Test #147: testMolAlign ........................... Passed 0.33 sec test 149 Start 149: molAlignCatchTest 149: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 149: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 123: Warning: Atom Count for residue ASN157A does not match expected count 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 149: Randomness seeded to: 2176915630 149: 93522919 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:3 139: [09:08:22] Rep: 40 Mol:7 139: [09:08:22] Rep: 40 Mol:11 139: [09:08:22] Rep: 40 Mol:15 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:19 139: [09:08:22] Rep: 40 Mol:23 139: [09:08:22] Rep: 40 Mol:27 139: [09:08:22] Rep: 40 Mol:31 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:2 139: [09:08:22] Rep: 40 Mol:6 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:10 139: [09:08:22] Rep: 40 Mol:14 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:18 139: [09:08:22] Rep: 40 Mol:22 139: [09:08:22] Rep: 40 Mol:26 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:30 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 149: 109508588 143: ... 143: ---------------------------------------------------------------------- 143: Ran 19 tests in 0.729s 143: 143: OK 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 60 Mol:1 139: [09:08:22] Rep: 60 Mol:5 139: [09:08:22] Rep: 60 Mol:9 139: [09:08:22] Rep: 60 Mol:13 139: [09:08:22] Rep: 60 Mol:17 139: [09:08:22] Rep: 60 Mol:21 139: [09:08:22] Rep: 60 Mol:25 139: [09:08:22] Rep: 60 Mol:29 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:0 139: [09:08:22] Rep: 40 Mol:4 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 40 Mol:8 139: [09:08:22] Rep: 40 Mol:12 139: [09:08:22] Rep: 40 Mol:16 139: [09:08:22] Rep: 40 Mol:20 139: [09:08:22] Rep: 40 Mol:24 139: [09:08:22] Rep: 40 Mol:28 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:22] Rep: 100 Mol:3 141: [09:08:22] Rep: 100 Mol:7 141: [09:08:22] Rep: 100 Mol:11 141: [09:08:22] Rep: 100 Mol:15 141: [09:08:22] Rep: 100 Mol:19 141: [09:08:22] Rep: 100 Mol:23 141: [09:08:22] Rep: 100 Mol:27 141: [09:08:22] Rep: 100 Mol:31 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:22] Rep: 60 Mol:3 139: [09:08:22] Rep: 60 Mol:7 139: [09:08:22] Rep: 60 Mol:11 139: [09:08:22] Rep: 60 Mol:15 139: [09:08:22] Rep: 60 Mol:19 139: [09:08:22] Rep: 60 Mol:23 139: [09:08:22] Rep: 60 Mol:27 139: [09:08:22] Rep: 60 Mol:31 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() 130/230 Test #143: pyForceFieldHelpers .................... Passed 2.22 sec test 150 Start 150: pyMolAlign 150: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 150: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 150: Test timeout computed to be: 1500 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:23] Rep: 80 Mol:1 139: [09:08:23] Rep: 80 Mol:5 139: [09:08:23] Rep: 80 Mol:9 139: [09:08:23] Rep: 80 Mol:13 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:23] Rep: 100 Mol:0 139: [09:08:23] Rep: 80 Mol:17 139: [09:08:23] Rep: 80 Mol:21 139: [09:08:23] Rep: 80 Mol:25 141: [09:08:23] Rep: 100 Mol:4 141: [09:08:23] Rep: 100 Mol:8 141: [09:08:23] Rep: 100 Mol:12 141: [09:08:23] Rep: 100 Mol:16 141: [09:08:23] Rep: 100 Mol:20 141: [09:08:23] Rep: 100 Mol:24 139: [09:08:23] Rep: 80 Mol:29 141: [09:08:23] Rep: 100 Mol:28 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 87: [09:08:23] Explicit valence for atom # 3 Al, 6, is greater than permitted 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:23] Rep: 60 Mol:2 139: [09:08:23] Rep: 60 Mol:6 139: [09:08:23] Rep: 60 Mol:10 139: [09:08:23] Rep: 60 Mol:14 139: [09:08:23] Rep: 60 Mol:18 139: [09:08:23] Rep: 60 Mol:22 139: [09:08:23] Rep: 60 Mol:26 139: [09:08:23] Rep: 60 Mol:30 146: .[09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:23] Rep: 100 Mol:2 141: [09:08:23] Rep: 100 Mol:6 141: [09:08:23] Rep: 100 Mol:10 141: [09:08:23] Rep: 100 Mol:14 141: [09:08:23] Rep: 100 Mol:18 141: [09:08:23] Rep: 100 Mol:22 141: [09:08:23] Rep: 100 Mol:26 141: [09:08:23] Rep: 100 Mol:30 139: [09:08:23] Rep: 80 Mol:3 139: [09:08:23] Rep: 80 Mol:7 139: [09:08:23] Rep: 80 Mol:11 139: [09:08:23] Rep: 80 Mol:15 139: [09:08:23] Rep: 80 Mol:19 139: [09:08:23] Rep: 80 Mol:23 139: [09:08:23] Rep: 80 Mol:27 139: [09:08:23] Rep: 80 Mol:31 87: [09:08:23] Explicit valence for atom # 4 Al, 6, is greater than permitted 27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 139: [09:08:23] Rep: 60 Mol:0 139: [09:08:23] Rep: 60 Mol:4 141: [09:08:23] Rep: 100 Mol:1 141: [09:08:23] Rep: 100 Mol:5 141: [09:08:23] Rep: 100 Mol:9 141: [09:08:23] Rep: 100 Mol:13 141: [09:08:23] Rep: 100 Mol:17 141: [09:08:23] Rep: 100 Mol:21 141: [09:08:23] Rep: 100 Mol:25 141: [09:08:23] Rep: 100 Mol:29 139: [09:08:23] Rep: 60 Mol:8 139: [09:08:23] Rep: 60 Mol:12 139: [09:08:23] Rep: 60 Mol:16 139: [09:08:23] Rep: 60 Mol:20 139: [09:08:23] Rep: 60 Mol:24 139: [09:08:23] Rep: 60 Mol:28 124: Warning: Atom Count for residue GLU150A does not match expected count 87: [09:08:23] Explicit valence for atom # 10 Si, 6, is greater than permitted 145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 6 145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 6 124: Warning: Atom Count for residue ASN157A does not match expected count 139: [09:08:23] Rep: 80 Mol:0 139: [09:08:23] Rep: 80 Mol:4 139: [09:08:23] Rep: 80 Mol:8 145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 6 139: [09:08:23] Rep: 80 Mol:12 139: [09:08:23] Rep: 80 Mol:16 139: [09:08:23] Rep: 80 Mol:20 139: [09:08:23] Rep: 80 Mol:24 139: [09:08:23] Rep: 80 Mol:28 139: [09:08:23] Rep: 80 Mol:2 139: [09:08:23] Rep: 80 Mol:6 139: [09:08:23] Rep: 80 Mol:10 139: [09:08:23] Rep: 80 Mol:14 145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 139: [09:08:23] Rep: 80 Mol:18 139: [09:08:23] Rep: 80 Mol:22 139: [09:08:23] Rep: 80 Mol:26 145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 139: [09:08:23] Rep: 80 Mol:30 145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() 149: 1411383903 27: All 191 tests passed 27: 27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 139: [09:08:24] done 139: [09:08:24] ------------------------------------- 139: [09:08:24] Test MMFF multithreading2 144: [09:08:20] --------------------------------- 144: [09:08:20] test3 144: 144: [09:08:20] --------------------------------- 144: [09:08:20] test4 144: 144: [09:08:20] --------------------------------- 144: [09:08:20] test5 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test6 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test15Dists 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test Issue 215 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testMultipleConfs 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testMultipleConfsExpTors 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testIssue227 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testIssue236 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testOrdering 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testIssue244 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testIssue251 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testIssue276 144: [09:08:24] --------------------------------- 144: [09:08:24] testIssue284 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testIssue285 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testIssue355 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] testRandomCoords 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test sf.net issue 1989539 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test sf.net issue 2091864 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test constrained embedding 144: 144: [09:08:24] ssd: 0.0752641 144: [09:08:24] ssd: 0.0659363 146: [09:08:24] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:24] done 141: [09:08:24] ------------------------------------- 141: [09:08:24] Test UFF multithreading2 87: [09:08:24] Explicit valence for atom # 2 O, 4, is greater than permitted 149: 878192114 149: =============================================================================== 149: All tests passed (73 assertions in 3 test cases) 149: 131/230 Test #149: molAlignCatchTest ...................... Passed 2.68 sec test 151 Start 151: testFeatures 151: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures 151: Test timeout computed to be: 1500 151: [09:08:24] ------------------------------------- 151: [09:08:24] AtomType parser testing. 151: [09:08:24] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] 151: [09:08:24] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' 151: [09:08:24] done 151: [09:08:24] ------------------------------------- 151: [09:08:24] FeatureDefinition parser testing. 151: [09:08:24] done 151: [09:08:24] ------------------------------------- 151: [09:08:24] Test pulling feat defs from a string. 151: [09:08:24] done 151: [09:08:24] ------------------------------------- 151: [09:08:24] FeatureDef functionality testing. 87: [09:08:24] Explicit valence for atom # 3 Al, 6, is greater than permitted 87: [09:08:24] Explicit valence for atom # 3 Be, 4, is greater than permitted 151: [09:08:25] done 151: [09:08:25] ------------------------------------- 151: [09:08:25] FeatureFactory testing. 151: [09:08:25] 1 151: [09:08:25] 2 151: [09:08:25] 3 151: [09:08:25] 4 151: [09:08:25] 5 151: [09:08:25] 6 151: [09:08:25] done 151: [09:08:25] ------------------------------------- 151: [09:08:25] Feature Location testing. 151: [09:08:25] done 151: [09:08:25] ------------------------------------- 151: [09:08:25] Test building a FeatureFactory from a file 151: [09:08:25] done 151: [09:08:25] ------------------------------------- 151: [09:08:25] Testing Issue 224. 151: [09:08:25] done 151: [09:08:25] ------------------------------------- 151: [09:08:25] Testing Issue 225. 151: [09:08:25] done 151: [09:08:25] ------------------------------------- 151: [09:08:25] Test Issue346 151: [09:08:25] done 151: [09:08:25] ------------------------------------- 151: [09:08:25] Test Issue347 151: [09:08:25] done 151: [09:08:25] ------------------------------------- 151: [09:08:25] Testing Issue 348. 151: [09:08:25] SMARTS Parse Error: syntax error while parsing: [C[C] 151: [09:08:25] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' 151: [09:08:25] ------------------------------------- 151: [09:08:25] Testing Nested AtomType definitions. 151: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] 151: [09:08:25] ------------------------------------- 151: [09:08:25] Testing Github Issue #252: crash when calling getPos() with no conformer. 151: [09:08:25] expect a precondition failure message below 151: [09:08:25] 151: 151: **** 151: Pre-condition Violation 151: molecule has no conformers 151: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 151: Failed Expression: dp_mol->getNumConformers() 151: ---------- 151: Stacktrace: 151: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 151: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 151: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 151: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 151: 4# 0x0000559F1AFA0E20 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: 5# 0x0000559F1AF956A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: 6# 0x00007F488C031D68 in /lib/x86_64-linux-gnu/libc.so.6 151: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 151: 8# 0x0000559F1AF957A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: ---------- 151: **** 151: 151: [09:08:25] Done 151: [09:08:25] ------------------------------------- 151: [09:08:25] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() 151: [09:08:25] done 132/230 Test #151: testFeatures ........................... Passed 0.08 sec test 152 Start 152: pyChemicalFeatures 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 152: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 152: Test timeout computed to be: 1500 87: [09:08:25] Explicit valence for atom # 27 P, 6, is greater than permitted 144: [09:08:24] --------------------------------- 144: [09:08:24] test sf.net issue 2091974 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test sf.net issue 2835784 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test sf.net issue 3019283 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test sf.net issue 3238580 144: 144: [09:08:24] --------------------------------- 144: [09:08:24] test sf.net issue 3483968 144: 144: [09:08:25] --------------------------------- 144: [09:08:25] test github issue 55 144: 144: [09:08:25] --------------------------------- 144: [09:08:25] test1 144: 144: [09:08:25] --------------------------------- 144: [09:08:25] test multi-threading 144: 144: building molecules 152: .[09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() 152: .[09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() 144: generating reference data 152: ..[09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() 87: =============================================================================== 87: All tests passed (21162 assertions in 3 test cases) 87: 152: .[09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() 152: .[09:08:25] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] 152: [09:08:25] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 152: ... 152: ---------------------------------------------------------------------- 152: Ran 9 tests in 0.124s 152: 152: OK 133/230 Test #87: multithreadedSupplierCatchTest ......... Passed 11.23 sec test 153 Start 153: testShapeHelpers 153: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 153: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 153: Test timeout computed to be: 1500 139: [09:08:25] done 139: [09:08:25] ------------------------------------- 139: [09:08:25] Test MMFF multithreading3 153: *********************************************************** 153: Testing ShapeHelpers 153: --------------------------------- 153: test1Encode 153: 153: --------------------------------- 153: test2Compare 153: 153: --------------------------------- 153: testGithub4364 153: 153: *********************************************************** 134/230 Test #153: testShapeHelpers ....................... Passed 0.09 sec test 154 Start 154: pyShapeHelpers 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 154: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 154: Test timeout computed to be: 1500 135/230 Test #152: pyChemicalFeatures ..................... Passed 0.70 sec test 155 Start 155: testMolCatalog 155: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 155: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 155: Test timeout computed to be: 1500 136/230 Test #155: testMolCatalog ......................... Passed 0.05 sec test 156 Start 156: pyMolCatalog 156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 156: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 156: Test timeout computed to be: 1500 146: [09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() 141: [09:08:26] done 141: [09:08:26] ------------------------------------- 141: [09:08:26] Test UFF multithreading3 146: [09:08:26] Molecule does not have explicit Hs. Consider calling AddHs() 115: =>start test GETAWAY custom 115: [09:08:26] test on : 365 molecules done 137/230 Test #115: testRDFcustom .......................... Passed 9.77 sec test 157 Start 157: moldraw2DTest1 157: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 157: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 157: Test timeout computed to be: 1500 157: ----------------- Test 1 157: file test1_5.svg gave hash 2383324771U not the expected 2811480876U 157: Done 157: ----------------- Test 2 157: file test2_1.png gave hash 2445376551U not the expected 307437906U 157: file test2_2.png gave hash 1007500626U not the expected 610424244U 157: Done 157: ----------------- Test 4 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Test GitHub Issue 258: Bad pattern fingerprint for query molecule 157: file test4_1.png gave hash 2289651897U not the expected 1403972924U 157: Done 157: ----------------- Test 5 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Test unfolded version of RDKFP 126: [09:08:26] ------------------------------------- 126: [09:08:26] Test bitinfo of RDKFP 126: 562: [ 2 ], 126: 709: [ 0 1 ], 126: 1118: [ 0 1 2 ], 126: 1183: [ 1 2 ], 126: 1233: [ 0 1 2 ], 126: 1308: [ 0 ], [ 1 ], 126: 1339: [ 2 ], 126: 1728: [ 1 2 ], 126: 1772: [ 0 ], [ 1 ], 126: 1813: [ 0 1 ], 126: ------------ 126: [09:08:26] ------------------------------------- 126: [09:08:26] Single atoms setting radius 1 bits in Morgan fingerprints 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Github #879: Pattern fingerprint should set bits for single-atom fragments. 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Github #2115: BitInfo not complete for RDKFingerprint 126: [09:08:26] done 126: [09:08:26] ------------------------------------- 126: [09:08:26] Github #3723: Fingerprint crash for mols with Zero order bonds 126: [09:08:26] done 138/230 Test #126: testFingerprints ....................... Passed 8.14 sec test 158 Start 158: moldraw2DTestCatch 158: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 158: Test timeout computed to be: 1500 154: . 154: ---------------------------------------------------------------------- 154: Ran 1 test in 0.206s 154: 154: OK 154: Testing Shape Helpers wrapper 157: file test5_1.png gave hash 1708884460U not the expected 1269428339U 157: file test5_2.png gave hash 263952708U not the expected 3073694291U 156: . 156: ---------------------------------------------------------------------- 156: Ran 1 test in 0.016s 156: 156: OK 157: file test5_3.png gave hash 2875214783U not the expected 1865192682U 139: [09:08:26] done 139: [09:08:26] ------------------------------------- 139: [09:08:26] Testing github 162: Incorrect SMILES after MMFF parameterization . 139: [09:08:26] done 139: [09:08:26] ------------------------------------- 139: [09:08:26] Testing github 224: crash during MMFF parameterization . 139: [09:08:26] done 139: [09:08:26] ------------------------------------- 139: [09:08:26] Testing github6728: crash due to missing stretch-bend params. 158: Randomness seeded to: 1047875229 158: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U 157: Done 157: ----------------- Test 6 (atom labels) 139/230 Test #139: testMMFFForceFieldHelpers .............. Passed 6.85 sec test 159 Start 159: moldraw2DRxnTest1 159: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 159: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 157: Done 157: ----------------- Test 7 (backgrounds) 140/230 Test #154: pyShapeHelpers ......................... Passed 1.23 sec test 160 Start 160: pyMolDraw2D 160: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 160: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 160: Test timeout computed to be: 1500 157: file test7_1.png gave hash 2503310706U not the expected 3033050306U 141/230 Test #156: pyMolCatalog ........................... Passed 1.17 sec test 161 Start 161: testFMCS 161: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 161: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 161: Test timeout computed to be: 1500 159: ----------------- Test 1 157: file test7_2.png gave hash 4294114077U not the expected 3476380724U 157: Done 157: ----------------- Test8: PrepareMolDrawing 157: Done 157: ----------------- Test multi-threaded drawing 157: reading molecules 73: [09:08:26] Finished: testSmiCorrectness() 73: [09:08:26] ----------------------------------------- 73: 73: [09:08:26] 73: ----------------------------------------- 159: file rxn_test1_1.png gave hash 1238594098U not the expected 1556334749U 157: generating reference drawings 158: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U 159: file rxn_test1_2.png gave hash 2408715353U not the expected 1924084263U 73: [09:08:27] Spurious data before the first property will be ignored 73: [09:08:27] Property will be truncated after the first blank line 73: [09:08:27] Property will be truncated after the first blank line 73: [09:08:27] Property will be truncated after the first blank line 158: file contourMol_2.svg gave hash 4241964660U not the expected 572669511U 141: [09:08:27] done 141: [09:08:27] ------------------------------------- 141: [09:08:27] Testing GitHubIssue62. 158: file contourMol_3.svg gave hash 1333854566U not the expected 936771429U 159: file rxn_test1_3.png gave hash 2702306328U not the expected 1644921059U 158: file contourMol_4.svg gave hash 4249475618U not the expected 3302971362U 141: [09:08:27] beta-lactam 39.6387 141: [09:08:27] cyclopropanone 174.698 141: [09:08:27] aziridine 337.986 141: [09:08:27] aziridinone 115.248 141: [09:08:27] isobutene 2.48217 141: [09:08:27] acetone 1.91788 158: file contourMol_5.svg gave hash 3954963517U not the expected 2230414999U 141: [09:08:27] cyclopentanone 10.1648 141: [09:08:27] cyclopropene 99.4921 141: [09:08:27] cyclobutene 41.0156 141: [09:08:27] cyclopropane 267.236 141: [09:08:27] gamma-lactam 15.7471 159: file rxn_test1_4.png gave hash 1047103464U not the expected 2471435686U 141: [09:08:27] trans-2,3-diphenylcyclopropan-1-one 203.398 159: file rxn_test1_5.png gave hash 867798763U not the expected 1428782307U 141: [09:08:27] cis-2,3-diphenylcyclopropan-1-one 206.852 158: file testGithub3226_1.png gave hash 2960456425U not the expected 2350054896U 141: [09:08:27] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 141: [09:08:27] cyclopropylidencyclobutane 218.879 159: file rxn_test1_6.png gave hash 3642317125U not the expected 483353696U 157: processing 157: launch :0 157: launch :1 157: launch :2 157: launch :3 158: file testGithub3226_2.png gave hash 903480972U not the expected 606206725U 141: [09:08:27] diphenylmethylidencyclobutane 79.6139 141: [09:08:27] done 141: [09:08:27] ------------------------------------- 141: [09:08:27] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. 141: [09:08:27] done 141: [09:08:27] ------------------------------------- 141: [09:08:27] Test square planar complexes 141: [09:08:27] done 141: [09:08:27] ------------------------------------- 141: [09:08:27] Test octahedral complexes 141: [09:08:27] done 142/230 Test #141: testUFFForceFieldHelpers ............... Passed 7.08 sec test 162 Start 162: pyFMCS 162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap/testFMCS.py" 162: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 162: Test timeout computed to be: 1500 158: file testGithub3226_3.png gave hash 1380525103U not the expected 2282880418U 159: file rxn_test1_7.png gave hash 1818284781U not the expected 528963379U 158: file testPNGMetadata_1.png gave hash 138627947U not the expected 2423299691U 159: file rxn_test1_7.svg gave hash 3432246161U not the expected 1389845691U 159: Done 159: ----------------- Test 2: some examples that caused problems in testing 159: file rxn_test2_1.png gave hash 1441990148U not the expected 399415052U 158: file testPNGMetadata_2.png gave hash 2913846030U not the expected 2803353117U 159: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C 159: file rxn_test2_2_1.png gave hash 1239682505U not the expected 1215378243U 159: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl 159: file rxn_test2_2_2.png gave hash 2733977819U not the expected 3645141778U 159: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 159: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 159: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C 159: file rxn_test2_2_3.png gave hash 3575777004U not the expected 551946805U 159: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC 159: file rxn_test2_2_4.png gave hash 4049234447U not the expected 4234617566U 159: Done 159: ----------------- Test 3: test reactant highlighting 158: [09:08:27] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:27] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U 158: [09:08:27] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:27] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: file rxn_test3_1.png gave hash 3887561208U not the expected 4176857511U 159: Done 159: ----------------- Test 4: some examples from SMARTS in testing 159: draw! 146: [09:08:27] Molecule does not have explicit Hs. Consider calling AddHs() 158: file testHandDrawn-1.png gave hash 3356982379U not the expected 698316547U 159: file rxn_test4_1.png gave hash 1743844008U not the expected 4187207676U 158: [09:08:27] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:27] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: done 158: file testHandDrawn-2.svg gave hash 1534109833U not the expected 4132716144U 158: [09:08:27] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:27] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-2.png gave hash 3620124651U not the expected 1605553248U 158: [09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-3.svg gave hash 2359787964U not the expected 4199337510U 158: [09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-3.png gave hash 1463224710U not the expected 2881952238U 158: [09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-4.svg gave hash 1880974760U not the expected 4197407865U 158: [09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: file rxn_test4_2.png gave hash 2769144016U not the expected 3490081297U 158: file testHandDrawn-4.png gave hash 2460067691U not the expected 3431655453U 159: Done 143/230 Test #159: moldraw2DRxnTest1 ...................... Passed 1.28 sec test 163 Start 163: FMCStest 163: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 163: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 163: Test timeout computed to be: 1500 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_15113.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_16613.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_30745.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_30861.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_31495.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_34869.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_36158.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_36559.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_37434.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_39147.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_43754.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_44011.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_44158.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_48076.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_48961.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_49648.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_49703.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_51128.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_51343.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_51842.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_54554.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_100_55749.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_17256.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20244.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20245.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30149.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30499.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_36186.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_39262.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_43966.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_45279.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_48029.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49064.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49801.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_50681.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_54039.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58265.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58358.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58866.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10188_60810.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21358.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21597.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30111.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30349.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31746.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31822.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_35220.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37603.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37964.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_39508.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42164.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42577.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_44072.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_45522.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46700.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46719.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46744.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_48517.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_49087.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_50034.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_51475.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53483.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53506.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_54598.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55614.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55737.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57090.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57705.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57785.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_58463.txt 163: 163: testChEMBfopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: L_Txt() chembl_II_sets/Target_no_10193_58700.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61003.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61349.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10260_38526.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10260_50778.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10260_52179.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10260_54285.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_30224.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_31222.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37349.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37369.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37465.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37541.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_38371.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44314.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44578.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_45765.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_46281.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_47928.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_50624.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51341.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51662.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51767.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53081.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53396.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53407.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_58823.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_59190.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_60672.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10280_61176.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10434_20905.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30074.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30175.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30423.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10434_31555.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10434_34878.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10434_35926.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10434_42168.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_20859.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_30060.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_30061.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_30606.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_30866.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_31249.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_34921.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_35188.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_36636.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_37466.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_39202.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_43952.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_49345.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_49591.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_49854.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_51416.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_53537.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_58879.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_60679.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_107_61269.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_20600.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_20859.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_30060.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_30606.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_30866.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_31558.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_35188.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_37466.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_43875.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_48911.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_49591.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_49854.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: no_108_57887.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_60679.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_108_6857.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_15478.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_20853.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30840.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30862.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30918.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30994.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31014.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31508.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31623.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35003.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35004.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35281.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35957.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36520.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36641.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_38586.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_44431.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_45093.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_51302.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5247.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_52937.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_57198.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5739.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_10980_6535.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20205.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20986.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_30091.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34698.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34705.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37038.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37272.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37447.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38909.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38953.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_39472.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_45825.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_47179.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49028.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49860.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_51984.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53395.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53826.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54121.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54530.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_55738.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_57725.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11140_58590.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11365_20432.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11365_30331.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11365_37956.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11365_48114.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11365_58566.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34731.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34818.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37318.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37339.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37564.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39504.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39561.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46082.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46089.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47349.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47757.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_51593.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_54754.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58262.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58958.txt 163: 163: testChEMBL_Txt(fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: ) chembl_II_sets/Target_no_114_16827.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_20503.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_20724.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_30254.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_30321.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_30572.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_31116.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_31281.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_31443.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_34747.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_34920.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_35040.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_36623.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_37136.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_37208.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_38298.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_38554.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_39088.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_39543.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_44049.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_44562.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_45180.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_45867.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_46087.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_46829.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_47546.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_48395.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_50461.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_50765.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_51669.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_52381.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_57231.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_114_58246.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_30999.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31021.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31650.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_35011.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_37014.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_44598.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_48446.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50614.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50615.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50618.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11534_51950.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11575_31616.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11575_38381.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11575_45757.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11575_46816.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11575_50701.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11575_54049.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11575_57890.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11575_61045.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11631_30194.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11631_31421.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11631_35538.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11631_55727.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11631_60676.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11631_61130.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_11631_6444.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_15623.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_20096.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_21591.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_30184.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_30380.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_30745.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_30861.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_31619.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_34869.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_35284.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_36158.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_36915.txt 163: 163: testChEMBL_Txfopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: t() chembl_II_sets/Target_no_121_37434.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_37541.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_37677.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_38837.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_39530.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_43793.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_44158.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_44164.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_44579.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_44593.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_44692.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_44914.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_45878.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_48050.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_48706.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_48944.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_48961.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_49880.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_50055.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_50512.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_51064.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_53537.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_55749.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_58879.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_121_6876.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12209_44664.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12209_46451.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12209_50640.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12209_56102.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12209_58015.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59089.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59092.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12209_61340.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12252_31458.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12252_38481.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12252_42104.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49475.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49933.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12252_50558.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_126_37249.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_126_39117.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_126_48227.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_126_48229.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_126_53969.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_126_54262.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_126_55353.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_126_61212.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20250.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20506.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20626.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20689.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_21358.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30158.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30349.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_34843.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_35220.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36318.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36800.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_39349.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45385.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45676.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46700.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46719.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_48517.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_52690.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_53483.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_55435.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_56102.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58015.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58375.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_1295fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: 2_58700.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_16724.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_2710.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_30128.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_31250.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_35519.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_36905.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_46788.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_4737.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_55736.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_13001_57473.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_16146.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_30313.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_30539.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_30653.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_30988.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_31179.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_31339.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_3525.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_36886.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_37020.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_38128.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_43952.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_45210.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_45899.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_47889.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_51800.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_53158.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_5330.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_55648.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_56096.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_57287.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_57399.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_57606.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_58470.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_130_60894.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_15010.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_20304.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_20542.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_20788.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_21358.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_30349.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_31103.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_31764.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_31822.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_35220.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_37964.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_42164.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_44072.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_45522.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_46719.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_46744.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_48416.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_49740.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_50034.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_50640.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_53483.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_53506.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_53814.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_55435.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_56074.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_56107.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_57090.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_57705.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_57785.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_57861.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_58583.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_59089.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_15_59092.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_20600.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_30764.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_34876.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_37427.tfopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: xt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_38266.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_45283.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_46990.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_47123.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_47900.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_48050.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_48062.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_48076.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_50718.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_50972.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_51372.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_51830.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_53049.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_53505.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_54021.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_54565.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_54570.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_57666.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_57890.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_58072.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_58634.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_58643.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_59080.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_59202.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_59346.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_60379.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_60385.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_165_61098.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_17045_31154.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_17045_35648.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_17045_48914.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_17045_51975.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_17045_52435.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_17045_55790.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_17045_58958.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_17045_61146.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20191.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20562.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20606.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20607.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30003.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30402.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30726.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30924.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31457.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31460.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31600.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31620.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31640.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31782.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31797.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31829.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31856.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34690.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34691.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34694.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_35712.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37497.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37539.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48070.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48219.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48824.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48902.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_52867.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_53534.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_54570.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_58727.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60159.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60661.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_30037.txt 163: 163: testChEMBL_Txt() chefopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: mbl_II_sets/Target_no_259_34734.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_35365.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_35787.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_36793.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_37845.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_38328.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_39374.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_43936.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_44059.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_44405.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_44424.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_45166.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_46158.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_46425.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_47187.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_48435.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_48817.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_48849.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_48957.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_48965.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_49519.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_49921.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_50392.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_50972.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_52405.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_52442.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_53169.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_54640.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_57207.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_58537.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_58920.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_259_60358.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_25_16077.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_25_34943.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_25_36391.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_25_36574.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_25_52906.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_25_54642.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_16385.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_20333.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_20774.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_35825.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_37637.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_47741.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_48567.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_48841.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_49589.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_50564.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_51201.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_53150.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_55747.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_43_58276.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_20813.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_2331.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_2391.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_30374.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_30512.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_30796.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_31058.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_31450.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_36609.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_36636.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_38266.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_43800.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_47621.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_49433.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_49550.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_49865.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_51005.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_52373.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_53878.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_57618.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_59484.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_6563.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_61_16845.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_61_37106.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_61_37272.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_61_47947.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_61_50754.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_61_55800.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_61_57380.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_65_35328.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_65_36137.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_65_38826.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_65_44596.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_65_51275.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_65_55671.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_20155.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_30616.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_30653.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_30988.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_31339.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_31527.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_31631.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_36047.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_36568.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_36636.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_37020.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_38128.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_43952.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_45210.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_47889.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_51064.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_51800.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_5330.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_57508.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_58470.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_72_60894.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_20730.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_20753.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_30097.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_30663.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_35365.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_35375.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_35918.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_36010.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_36780.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_36793.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_37845.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_39110.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_39546.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_43936.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_44405.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_44424.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_44683.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_45166.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_46648.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_46986.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_47070.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_47187.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_48435.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_48817.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_49138.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_49460.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_49519.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_49532.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_49829.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_50608.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_54640.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_87_61082.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_90_15727.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_90_20155.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_90_30407.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_90_3525.txt 163: 163: testChEMBfopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: L_Txt() chembl_II_sets/Target_no_93_12377.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_93_1308.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_93_34759.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_93_35447.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_93_42214.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_93_45877.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_93_47082.txt 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_93_57082.txt 163: 163: testFileSDF_RandomSet(): benchmark/chembl13-10000-random-pairs.sdf 163: ERROR: RDKit could not load input file 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_pairs.smi 163: ERROR: RDKit could not load input file 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_knearest_2.smi 163: ERROR: RDKit could not load input file 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_knearest_10.smi 163: ERROR: RDKit could not load input file 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_knearest_100.smi 163: ERROR: RDKit could not load input file 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_threshold_80.smi 163: ERROR: RDKit could not load input file 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 163: ERROR: RDKit could not load input file 144/230 Test #163: FMCStest ............................... Passed 0.09 sec test 164 Start 164: molHashCatchTest 164: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 164: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash 164: Test timeout computed to be: 1500 160: ...[09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. 160: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 146: [09:08:28] Molecule does not have explicit Hs. Consider calling AddHs() 164: Randomness seeded to: 1788033641 164: =============================================================================== 164: All tests passed (332 assertions in 13 test cases) 164: 145/230 Test #164: molHashCatchTest ....................... Passed 0.12 sec test 165 Start 165: pyMolHash 165: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/Wrap/testMolHash.py" 165: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 165: Test timeout computed to be: 1500 160: ..........[09:08:28] 160: 160: **** 160: Pre-condition Violation 160: molecule must not be None 160: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp 160: Failed Expression: m 160: ---------- 160: Stacktrace: 160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 160: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 160: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 160: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 160: 5# 0x00007FC28A37B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 160: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 160: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 160: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 160: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 160: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 160: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 160: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 160: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 160: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 160: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 160: 16# 0x00007FC2899AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 160: 17# 0x00007FC2899AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 160: 18# 0x00007FC2899AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 160: 19# 0x00007FC2899AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 160: 20# 0x00007FC2899AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 160: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 160: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 160: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 160: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 160: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 160: 26# 0x00007FC28A3783C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 160: 27# _PyObject_MakeTpCall in /usr/bin/python3 160: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 29# 0x0000000000546E76 in /usr/bin/python3 160: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 31# _PyObject_Call_Prepend in /usr/bin/python3 160: 32# 0x000000000059D6E4 in /usr/bin/python3 160: 33# _PyObject_MakeTpCall in /usr/bin/python3 160: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 35# 0x0000000000546E76 in /usr/bin/python3 160: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 37# _PyObject_Call_Prepend in /usr/bin/python3 160: 38# 0x000000000059D6E4 in /usr/bin/python3 160: 39# _PyObject_MakeTpCall in /usr/bin/python3 160: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 41# 0x0000000000546E76 in /usr/bin/python3 160: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 43# _PyObject_Call_Prepend in /usr/bin/python3 160: 44# 0x000000000059D6E4 in /usr/bin/python3 160: 45# _PyObject_MakeTpCall in /usr/bin/python3 160: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 47# _PyObject_Call_Prepend in /usr/bin/python3 160: 48# 0x000000000059810D in /usr/bin/python3 160: 49# 0x0000000000593E22 in /usr/bin/python3 160: 50# _PyObject_MakeTpCall in /usr/bin/python3 160: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 52# PyEval_EvalCode in /usr/bin/python3 160: 53# 0x00000000005FFE7F in /usr/bin/python3 160: 54# 0x00000000006A59F2 in /usr/bin/python3 160: 55# _PyRun_SimpleFileObject in /usr/bin/python3 160: 56# _PyRun_AnyFileObject in /usr/bin/python3 160: 57# Py_RunMain in /usr/bin/python3 160: 58# Py_BytesMain in /usr/bin/python3 160: 59# 0x00007FC28CBF1D68 in /lib/x86_64-linux-gnu/libc.so.6 160: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 160: 61# _start in /usr/bin/python3 160: ---------- 160: **** 160: 73: [09:08:28] Finished: testSDCorrectness() 73: [09:08:28] ----------------------------------------- 73: 146/230 Test #73: testMultithreadedMolSupplier ........... Passed 14.75 sec test 166 Start 166: testMMPA 166: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 166: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 166: Test timeout computed to be: 1500 166: 166: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 166: Time elapsed 0.005569 seconds 166: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 166: 1: NOREF. Reference data NOT LISTED in test case. 166: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 166: 2: NOREF. Reference data NOT LISTED in test case. 166: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 166: 3: NOREF. Reference data NOT LISTED in test case. 166: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 166: 4: NOREF. Reference data NOT LISTED in test case. 166: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 166: 5: NOREF. Reference data NOT LISTED in test case. 166: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 166: 6: NOREF. Reference data NOT LISTED in test case. 166: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 166: 7: NOREF. Reference data NOT LISTED in test case. 166: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 166: 8: NOREF. Reference data NOT LISTED in test case. 166: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 166: 9: NOREF. Reference data NOT LISTED in test case. 166: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 166: 10: NOREF. Reference data NOT LISTED in test case. 166: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 166: 11: NOREF. Reference data NOT LISTED in test case. 166: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 166: 12: NOREF. Reference data NOT LISTED in test case. 166: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 166: 13: NOREF. Reference data NOT LISTED in test case. 166: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 166: 14: NOREF. Reference data NOT LISTED in test case. 166: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 166: 15: NOREF. Reference data NOT LISTED in test case. 166: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 166: 16: NOREF. Reference data NOT LISTED in test case. 166: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 166: 17: NOREF. Reference data NOT LISTED in test case. 166: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 166: 18: NOREF. Reference data NOT LISTED in test case. 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 166: ----------------------------------- 166: Time elapsed 0.008951 seconds 166: 166: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 166: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 166: 1: PASSED. matchedRefRes = 4 166: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 166: 2: PASSED. matchedRefRes = 1 166: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 166: 3: PASSED. matchedRefRes = 6 166: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 166: 4: PASSED. matchedRefRes = 13 166: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 166: 5: PASSED. matchedRefRes = 12 166: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 166: 6: PASSED. matchedRefRes = 10 166: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 160: ...................... 160: ---------------------------------------------------------------------- 160: Ran 35 tests in 0.548s 160: 160: OK 160: json lasso 166: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 10: PASSED. matchedRefRes = 3 166: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 12: PASSED. matchedRefRes = 8 166: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 13: PASSED. matchedRefRes = 9 166: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 14: PASSED. matchedRefRes = 11 166: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 15: PASSED. matchedRefRes = 2 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 166: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 166: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 166: ----------------------------------- 166: 166: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 166: Time elapsed 0.013863 seconds 166: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 166: 1: PASSED. matchedRefRes = 4 166: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 166: 2: PASSED. matchedRefRes = 1 166: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 166: 3: PASSED. matchedRefRes = 6 146: [09:08:28] Molecule does not have explicit Hs. Consider calling AddHs() 166: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 166: 4: PASSED. matchedRefRes = 13 166: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 166: 5: PASSED. matchedRefRes = 12 166: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 166: 6: PASSED. matchedRefRes = 10 166: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 7: NOREF. Reference data NOT LISTED in test case. 166: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 8: NOREF. Reference data NOT LISTED in test case. 166: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 9: NOREF. Reference data NOT LISTED in test case. 166: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 10: PASSED. matchedRefRes = 3 166: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 11: NOREF. Reference data NOT LISTED in test case. 166: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 12: PASSED. matchedRefRes = 8 166: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 13: PASSED. matchedRefRes = 9 166: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 14: PASSED. matchedRefRes = 11 166: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 15: PASSED. matchedRefRes = 2 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 166: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 166: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 166: ----------------------------------- 166: 166: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE 166: Time elapsed 0.004821 seconds 166: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 166: 1: PASSED. matchedRefRes = 2 166: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 166: 2: PASSED. matchedRefRes = 3 166: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 166: 3: NOREF. Reference data NOT LISTED in test case. 166: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] 166: 4: PASSED. matchedRefRes = 4 166: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 166: 5: PASSED. matchedRefRes = 5 166: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 166: 6: NOREF. Reference data NOT LISTED in test case. 166: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 166: 7: PASSED. matchedRefRes = 7 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] 166: 6: CC(N1CC1)C(=O),Case1-SIMPLE,CC([*:1])[*:2],C1CN1[*:1].O=C[*:2] 166: ----------------------------------- 166: 166: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 166: Time elapsed 0.009966 seconds 166: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 166: 1: NOREF. Reference data NOT LISTED in test case. 166: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 166: 2: NOREF. Reference data NOT LISTED in test case. 166: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 166: 3: NOREF. Reference data NOT LISTED in test case. 166: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 166: 4: NOREF. Reference data NOT LISTED in test case. 166: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 166: 5: NOREF. Reference data NOT LISTED in test case. 166: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 166: 6: NOREF. Reference data NOT LISTED in test case. 166: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 166: 7: NOREF. Reference data NOT LISTED in test case. 166: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 166: 8: NOREF. Reference data NOT LISTED in test case. 166: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 166: 9: NOREF. Reference data NOT LISTED in test case. 166: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 166: 10: NOREF. Reference data NOT LISTED in test case. 166: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 166: 11: NOREF. Reference data NOT LISTED in test case. 166: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 166: 12: NOREF. Reference data NOT LISTED in test case. 166: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 166: 13: NOREF. Reference data NOT LISTED in test case. 166: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 166: 14: NOREF. Reference data NOT LISTED in test case. 166: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 166: 15: NOREF. Reference data NOT LISTED in test case. 166: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 166: 16: NOREF. Reference data NOT LISTED in test case. 166: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 166: 17: NOREF. Reference data NOT LISTED in test case. 166: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 166: 18: NOREF. Reference data NOT LISTED in test case. 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 166: ----------------------------------- 166: 166: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 166: Time elapsed 0.014857 seconds 166: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 166: 1: NOREF. Reference data NOT LISTED in test case. 166: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 166: 2: NOREF. Reference data NOT LISTED in test case. 166: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 166: 3: NOREF. Reference data NOT LISTED in test case. 166: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 166: 4: NOREF. Reference data NOT LISTED in test case. 166: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 166: 5: NOREF. Reference data NOT LISTED in test case. 166: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 166: 6: NOREF. Reference data NOT LISTED in test case. 166: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 166: 7: NOREF. Reference data NOT LISTED in test case. 166: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 166: 8: NOREF. Reference data NOT LISTED in test case. 166: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 166: 9: NOREF. Reference data NOT LISTED in test case. 166: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 166: 10: NOREF. Reference data NOT LISTED in test case. 166: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 166: 11: NOREF. Reference data NOT LISTED in test case. 166: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 166: 12: NOREF. Reference data NOT LISTED in test case. 166: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 166: 13: NOREF. Reference data NOT LISTED in test case. 166: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 166: 14: PASSED. matchedRefRes = 1 166: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 166: 15: NOREF. Reference data NOT LISTED in test case. 166: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 166: 16: NOREF. Reference data NOT LISTED in test case. 166: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 166: 17: NOREF. Reference data NOT LISTED in test case. 166: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 166: 18: NOREF. Reference data NOT LISTED in test case. 166: 166: --- ALL PASSED --- 166: ----------------------------------- 166: 5 TEST CASES FAILED 147/230 Test #166: testMMPA ............................... Passed 0.36 sec test 167 Start 167: pyMMPA 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap/testMMPA.py" 167: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap 167: Test timeout computed to be: 1500 148/230 Test #160: pyMolDraw2D ............................ Passed 2.11 sec test 168 Start 168: testRascalMCES 168: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 168: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES 168: Test timeout computed to be: 1500 144: validating reference data 165: .... 165: ---------------------------------------------------------------------- 165: Ran 4 tests in 0.019s 165: 165: OK 146: [09:08:29] Molecule does not have explicit Hs. Consider calling AddHs() 148: *********************************************************** 148: Testing O3AAlign 148: --------------------------------- 148: testMMFFO3A 148: 148: --------------------------------- 148: testMMFFO3A with pre-computed dmat and MolHistogram 148: 148: --------------------------------- 148: testMMFFO3A with constraints 148: 148: --------------------------------- 148: testMMFFO3A with variable weight constraints followed by local-only optimization 148: 148: --------------------------------- 148: testCrippenO3A 148: 148: --------------------------------- 148: testCrippenO3A with pre-computed dmat and MolHistogram 148: 148: --------------------------------- 148: testCrippenO3A with constraints 148: 148: --------------------------------- 148: testCrippenO3A with variable weight constraints followed by local-only optimization 148: 148: --------------------------------- 148: testMMFFO3A multithreading 148: 148: generating reference data 149/230 Test #165: pyMolHash .............................. Passed 0.99 sec test 169 Start 169: testRascalCluster 169: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 169: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES 169: Test timeout computed to be: 1500 146: [09:08:29] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:08:30] Molecule does not have explicit Hs. Consider calling AddHs() 161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 161: Time elapsed 0.000 seconds 161: 161: test32() 161: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds 161: Time elapsed 0.069 seconds 161: 161: test190() 161: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds 161: Time elapsed 0.009 seconds 161: 161: test3() 161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds 161: Time elapsed 0.015 seconds 161: 161: testSimpleFast() 161: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds 161: Time elapsed 0.118 seconds 161: 161: testSimple() 161: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 161: Time elapsed 0.120 seconds 161: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 161: Time elapsed 0.270 seconds 161: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 161: Time elapsed 0.255 seconds 161: 161: testSegFault() 161: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 161: Time elapsed 0.018 seconds 161: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 161: Time elapsed 0.029 seconds 161: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds 161: Time elapsed 0.020 seconds 161: 161: testThreshold() 161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 161: Time elapsed 0.000 seconds 161: 161: testRing1() 161: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds 161: Time elapsed 0.761 seconds 161: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds 161: Time elapsed 0.929 seconds 161: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds 161: Time elapsed 0.472 seconds 161: 161: testAtomCompareIsotopes() 161: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds 161: Time elapsed 0.000 seconds 161: 161: testAtomCompareAnyAtom() 161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 161: Time elapsed 0.000 seconds 161: 161: testAtomCompareAnyAtom() 161: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 161: Time elapsed 0.000 seconds 161: 161: testAtomCompareAnyAtom() 161: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds 161: Time elapsed 0.000 seconds 161: 161: testAtomCompareAnyAtom() 161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds 161: Time elapsed 0.000 seconds 161: 161: testJnk1LigandsDistance() 161: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds 161: Time elapsed 0.011 seconds 161: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds 161: Time elapsed 0.002 seconds 161: 161: test18() 161: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 161: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds 161: Time elapsed 0.008 seconds 161: 161: test504() 161: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 161: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds 161: Time elapsed 0.108 seconds 161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 161: Time elapsed 0.002 seconds 161: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds 161: Time elapsed 0.033 seconds 161: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds 161: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0014 seconds. bond[0]=6 161: STATISTICS: 161: Total Growing Steps = 1, MCS found on 1 step, for 0.0014 seconds 161: Initial Seeds = 1, Mismatched 0 161: Inspected Seeds = 2 161: Rejected by BestSize = 0 161: IndividualBondExcluded = 0 161: MatchCheck Seeds = 2 161: MatchCalls = 2 161: MatchFound = 1 161: fastMatchCalls = 1 161: fastMatchFound = 0 161: slowMatchCalls = 2 161: slowMatchFound = 1 161: DupCacheFound = 0 0 matched, 0 mismatched 161: HashCache size = 1 keys 161: HashCache size = 1 entries 161: FindHashInCache = 2 161: HashFoundInCache= 0 161: ExactMatchCalls = 0 161: ExactMatchFound = 0 161: Time elapsed 0.002 seconds 161: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 161: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 161: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 161: res sub = 1 size=3 161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 161: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 161: res sub = 1 size=3 161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 161: test target = CC[C@H](F)Cl query = CCC useChirality = 0 161: res sub = 1 size=3 161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 161: test target = CC[C@H](F)Cl query = CCC useChirality = 1 161: res sub = 1 size=3 161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 161: test target = CCC(F)Cl query = CC useChirality = 0 161: res sub = 1 size=2 161: MCS: [#6]-[#6] 2 atoms, 1 bonds 161: test target = CCC(F)Cl query = CC useChirality = 1 161: res sub = 1 size=2 161: MCS: [#6]-[#6] 2 atoms, 1 bonds 161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 161: res sub = 1 size=4 161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 161: res sub = 1 size=4 161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 161: res sub = 1 size=4 161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 161: res sub = 1 size=4 161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 161: res sub = 0 size=0 161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 161: res sub = 0 size=0 161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 161: res sub = 0 size=0 161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 161: test target = OC(F)CCl query = OC(F)C useChirality = 0 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = OC(F)CCl query = OC(F)C useChirality = 1 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 161: res sub = 0 size=0 161: MCS: [#9] 1 atoms, 0 bonds 161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 161: res sub = 1 size=4 161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 161: res sub = 0 size=0 161: MCS: [#9] 1 atoms, 0 bonds 161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 161: res sub = 1 size=3 161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 161: res sub = 1 size=3 161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 161: res sub = 1 size=3 161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 161: res sub = 1 size=3 161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 161: 161: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> 161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 161: res sub = 1 size=3 161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 161: res sub = 1 size=3 161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 161: done 158: file testHandDrawn-5a.svg gave hash 1022103754U not the expected 3628607349U 158: [09:08:30] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:30] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-5b.svg gave hash 541506982U not the expected 2522138089U 158: [09:08:30] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. 158: [09:08:30] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-5.png gave hash 3431298533U not the expected 3439548169U 158: file testBrackets-5a.svg gave hash 279553678U not the expected 3061667963U 158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 158: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 174339626U 158: [09:08:31] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U 158: file testGithub4238_1.png gave hash 1615966361U not the expected 3410617836U 158: file testGithub4323_1.png gave hash 4251183326U not the expected 3723958844U 158: file testGithub4323_3.png gave hash 304742911U not the expected 2185913679U 158: [09:08:31] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 146: .[09:08:31] Molecule does not have explicit Hs. Consider calling AddHs() 161: [09:08:31] The provided InitialSeed is not an MCS and will be ignored 144: processing 144: launch :0 144: launch :1 144: launch :2 144: launch :3 158: file testFlexiCanvas.2a.png gave hash 4288280796U not the expected 3217758043U 158: file testFlexiCanvas.2b.png gave hash 3583431125U not the expected 4070063910U 158: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U 148: processing 148: launch :0 148: launch :1 148: launch :2 148: launch :3 93: 0,0 0 93: 0,1 0 93: 1,0 0 93: 1,1 0 93: 2,0 0 93: 2,1 0 150/230 Test #93: testEnumeration ........................ Passed 18.69 sec test 170 Start 170: pyRascalMCES 170: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 170: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 170: Test timeout computed to be: 1500 158: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U 158: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U 158: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U 158: file testGithub4764.sz1.png gave hash 1930422547U not the expected 98827714U 158: file testGithub4764.sz2.png gave hash 2441829654U not the expected 89252465U 158: file testGithub4764.sz3.png gave hash 3374802290U not the expected 148503574U 158: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U 158: file github5383_1.svg gave hash 4241964660U not the expected 3666750661U 158: file github5383_2.svg gave hash 2560846108U not the expected 0U 158: file github5383_1.png gave hash 2818284953U not the expected 992803933U 158: file acs1996_1.png gave hash 342575424U not the expected 2957839025U 158: file acs1996_2.svg gave hash 908745273U not the expected 1521279517U 158: file acs1996_2.png gave hash 496998965U not the expected 2664798808U 158: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U 158: file acs1996_5.svg gave hash 3624853279U not the expected 1680320774U 158: file acs1996_8.svg gave hash 4110469272U not the expected 2477908768U 158: file acs1996_9.svg gave hash 231896677U not the expected 3747924004U 158: [09:08:33] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. 158: file bond_highlights_8.svg gave hash 682598716U not the expected 2956924065U 158: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U 170: ..........Too many matching bond pairs (1032) so can't continue. 158: file test_github6200_1.svg gave hash 1975293465U not the expected 1044179149U 158: file test_github6397_2.svg gave hash 2405824082U not the expected 3422233570U 158: file test_github6397_3.svg gave hash 759740391U not the expected 3320683230U 158: file test_github6397_4.svg gave hash 2454933776U not the expected 2960192928U 158: file test_github6397_5.svg gave hash 1843492326U not the expected 1245534660U 123: Warning: Atom Count for residue GLU5A does not match expected count 123: Warning: Atom Count for residue ASN39A does not match expected count 123: Warning: Atom Count for residue GLU53A does not match expected count 123: Warning: Atom Count for residue ARG64A does not match expected count 123: Warning: Atom Count for residue LYS80A does not match expected count 158: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U 123: Warning: Atom Count for residue GLU150A does not match expected count 123: Warning: Atom Count for residue ASN157A does not match expected count 158: file github6504_2.svg gave hash 106020287U not the expected 2871662880U 158: file github6569_1.svg gave hash 1698514747U not the expected 116573839U 158: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U 123: =============================================================================== 123: All tests passed (515 assertions in 10 test cases) 123: 151/230 Test #123: descriptorsTestCatch ................... Passed 17.13 sec test 171 Start 171: testCIPLabeler 171: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 171: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler 171: Test timeout computed to be: 1500 167: ......... 167: ---------------------------------------------------------------------- 167: Ran 9 tests in 5.529s 167: 167: OK 171: Randomness seeded to: 3980464096 171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 171: [09:08:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 171: [09:08:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 152/230 Test #167: pyMMPA ................................. Passed 6.71 sec test 172 Start 172: pyCIPLabelsWrapTest 172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 172: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 172: Test timeout computed to be: 1500 171: =============================================================================== 171: All tests passed (6572 assertions in 18 test cases) 171: 153/230 Test #171: testCIPLabeler ......................... Passed 0.43 sec test 173 Start 173: pyCIPLabelsValidation 173: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 173: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 173: Test timeout computed to be: 1500 172: .... 172: ---------------------------------------------------------------------- 172: Ran 4 tests in 0.044s 172: 172: OK 154/230 Test #172: pyCIPLabelsWrapTest .................... Passed 1.13 sec test 174 Start 174: deprotectTest 174: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 174: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect 174: Test timeout computed to be: 1500 174: Randomness seeded to: 2874380384 174: =============================================================================== 174: All tests passed (111 assertions in 3 test cases) 174: 155/230 Test #174: deprotectTest .......................... Passed 0.11 sec test 175 Start 175: pyDeprotect 175: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Wrap/rough_test.py" 175: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 175: Test timeout computed to be: 1500 158: file AtropCanon1.svg gave hash 818325437U not the expected 526339583U 158: file AtropManyChiralsEnhanced.svg gave hash 3759358369U not the expected 348414093U 158: file testGithub6968.svg gave hash 940962291U not the expected 1554428830U 170: ... 170: ---------------------------------------------------------------------- 170: Ran 13 tests in 3.138s 170: 170: OK 156/230 Test #170: pyRascalMCES ........................... Passed 4.26 sec test 176 Start 176: testReducedGraphs 176: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 176: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs 176: Test timeout computed to be: 1500 158: file testWedgeNonSingleBonds-1.svg gave hash 2116685919U not the expected 865601717U 158: file testWedgeNonSingleBonds-2.svg gave hash 1174395532U not the expected 2960559495U 158: file testWedgeNonSingleBonds-3.svg gave hash 2542970771U not the expected 1428196589U 158: file testWedgeNonSingleBonds-4.svg gave hash 700876833U not the expected 3897680387U 158: file testWedgeNonSingleBonds-5.svg gave hash 2012191155U not the expected 2183530217U 158: file testWedgeNonSingleBonds-6.svg gave hash 2517061935U not the expected 238313010U 158: file testWedgeNonSingleBonds-7.svg gave hash 157069219U not the expected 3641456570U 158: file testWedgeNonSingleBonds-8.svg gave hash 3431784338U not the expected 3209701539U 176: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 176: 176: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 176: 176: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 176: 176: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, ] 176: 176: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 176: 176: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 176: 176: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 176: 157/230 Test #176: testReducedGraphs ...................... Passed 0.05 sec test 177 Start 177: pyReducedGraphs 177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 177: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 177: Test timeout computed to be: 1500 175: ..... 175: ---------------------------------------------------------------------- 175: Ran 5 tests in 0.116s 175: 175: OK 175: Testing tert-butyldimethylsilyl 175: Testing methoxytrityl 175: Testing tetrahydropyranyl 175: Testing methoxymethyl_ether 175: Testing beta-Methoxyethoxymethyl_ether 175: Testing benzyl 175: Testing trimethylsilyl 175: Testing benzoyl 175: Testing pivaloyl 175: Testing triisopropylsilyl 175: Testing acetyl 175: Testing para-methoxybenzyl_ether 175: Testing triphenylmethyl 175: Testing phthaloyl 175: Testing trimethylsilylethoxymethyl 175: Testing para-methoxyphenyl 175: Testing tosyl 175: Testing tert-butyloxycarbonyl 175: Testing trifluoroacetyl 175: Testing benzoyl 175: Testing 9-fluorenylmethyloxycarbonyl 175: Testing benzylamine 175: Testing acetamide 175: Testing carbobenzyloxy 175: Testing Acetal/Ketal 175: Testing tert-butyldimethylsilyl 175: Testing methoxytrityl 175: Testing tetrahydropyranyl 175: Testing methoxymethyl_ether 175: Testing beta-Methoxyethoxymethyl_ether 175: Testing benzyl 175: Testing trimethylsilyl 175: Testing benzoyl 175: Testing pivaloyl 175: Testing triisopropylsilyl 175: Testing acetyl 175: Testing para-methoxybenzyl_ether 175: Testing triphenylmethyl 175: Testing phthaloyl 175: Testing trimethylsilylethoxymethyl 175: Testing para-methoxyphenyl 175: Testing tosyl 175: Testing tert-butyloxycarbonyl 175: Testing trifluoroacetyl 175: Testing benzoyl 175: Testing 9-fluorenylmethyloxycarbonyl 175: Testing benzylamine 175: Testing acetamide 175: Testing carbobenzyloxy 175: Testing Acetal/Ketal 158: file testGithub_7739_1.svg gave hash 1477601334U not the expected 52079325U 158/230 Test #175: pyDeprotect ............................ Passed 0.79 sec test 178 Start 178: trajectoryTest 178: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 178: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory 178: Test timeout computed to be: 1500 124: Warning: Atom Count for residue GLU5A does not match expected count 124: Warning: Atom Count for residue ASN39A does not match expected count 124: Warning: Atom Count for residue GLU53A does not match expected count 124: Warning: Atom Count for residue ARG64A does not match expected count 124: Warning: Atom Count for residue LYS80A does not match expected count 124: Warning: Atom Count for residue GLU150A does not match expected count 124: Warning: Atom Count for residue ASN157A does not match expected count 124: .[09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: .[09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: ..[09:08:37] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator 124: .[09:08:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: ...[09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator 158: file testGithub_7739_3.svg gave hash 4066656179U not the expected 1126644226U 124: ....[09:08:37] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator 124: ....[09:08:38] DEPRECATION WARNING: please use AtomPairGenerator 124: [09:08:38] DEPRECATION WARNING: please use AtomPairGenerator 124: .[09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: ..[09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: .[09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: ... 124: ---------------------------------------------------------------------- 124: Ran 31 tests in 19.155s 124: 124: OK 124: exactmw 78.046950192 124: amw 78.11399999999999 124: lipinskiHBA 0.0 124: lipinskiHBD 0.0 124: NumRotatableBonds 0.0 124: NumHBD 0.0 124: NumHBA 0.0 124: NumHeavyAtoms 6.0 124: NumAtoms 6.0 124: NumHeteroatoms 0.0 124: NumAmideBonds 0.0 124: FractionCSP3 0.0 124: NumRings 1.0 124: NumAromaticRings 1.0 124: NumAliphaticRings 0.0 124: NumSaturatedRings 0.0 124: NumHeterocycles 0.0 124: NumAromaticHeterocycles 0.0 124: NumSaturatedHeterocycles 0.0 124: NumAliphaticHeterocycles 0.0 124: NumSpiroAtoms 0.0 124: NumBridgeheadAtoms 0.0 124: NumAtomStereoCenters 0.0 124: NumUnspecifiedAtomStereoCenters 0.0 124: labuteASA 37.43140311949697 124: tpsa 0.0 124: CrippenClogP 1.6866 124: CrippenMR 26.441999999999993 124: chi0v 3.464101615137755 124: chi1v 2.0000000000000004 124: chi2v 0.6666666666666671 124: chi3v 0.6666666666666671 124: chi4v 0.38490017945975075 124: chi0n 3.464101615137755 124: chi1n 2.0000000000000004 124: chi2n 0.6666666666666671 124: chi3n 0.6666666666666671 124: chi4n 0.38490017945975075 124: hallKierAlpha -0.78 124: kappa1 3.4115708812260532 124: kappa2 1.6057694396735218 124: kappa3 0.5823992601400448 124: Phi 0.9130327103921437 124: exactmw 78.046950192 124: lipinskiHBA 0.0 158: file testGithub_7739_4.svg gave hash 1029970961U not the expected 9844878U 158: [09:08:38] 158: 158: **** 158: Pre-condition Violation 158: 158: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp 158: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() 158: ---------- 158: Stacktrace: 158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 158: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 8# 0x000055B20506F715 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 9# 0x000055B205148548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 10# 0x000055B205149068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 11# 0x000055B2051494E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 12# 0x000055B20511B203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 13# 0x000055B20511B56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 14# 0x000055B20506824E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 15# 0x00007F4A8BC31D68 in /lib/x86_64-linux-gnu/libc.so.6 158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 158: 17# 0x000055B205068291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: ---------- 158: **** 158: 158: [09:08:38] 158: 158: **** 158: Range Error 158: idx 158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp 158: Failed Expression: 2 < 0 158: ---------- 158: Stacktrace: 158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 8# 0x000055B20506EE82 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 9# 0x000055B205148548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 10# 0x000055B205149068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 11# 0x000055B2051494E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 12# 0x000055B20511B203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 13# 0x000055B20511B56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 14# 0x000055B20506824E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 15# 0x00007F4A8BC31D68 in /lib/x86_64-linux-gnu/libc.so.6 158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 158: 17# 0x000055B205068291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: ---------- 158: **** 158: 158: [09:08:38] 158: 158: **** 158: Range Error 158: idx 158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp 158: Failed Expression: 0 < 0 158: ---------- 158: Stacktrace: 158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 8# 0x000055B20506F7E8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 9# 0x000055B205148548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 10# 0x000055B205149068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 11# 0x000055B2051494E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 12# 0x000055B20511B203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 13# 0x000055B20511B56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 14# 0x000055B20506824E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: 15# 0x00007F4A8BC31D68 in /lib/x86_64-linux-gnu/libc.so.6 158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 158: 17# 0x000055B205068291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: ---------- 158: **** 158: 158: =============================================================================== 158: All tests passed (6801 assertions in 105 test cases) 158: 159/230 Test #158: moldraw2DTestCatch ..................... Passed 11.49 sec test 179 Start 179: substructLibraryTest 179: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 179: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 179: Test timeout computed to be: 1500 160/230 Test #124: pyMolDescriptors ....................... Passed 19.90 sec test 180 Start 180: substructLibraryCatchTest 180: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 180: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 180: Test timeout computed to be: 1500 179: [09:08:38] ------------------------------------- 179: [09:08:38] Test1 177: ..... 177: ---------------------------------------------------------------------- 177: Ran 5 tests in 0.023s 177: 177: OK 161/230 Test #177: pyReducedGraphs ........................ Passed 0.82 sec test 181 Start 181: pySubstructLibrary 181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 181: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 181: Test timeout computed to be: 1500 169: Randomness seeded to: 1676980870 169: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data/chembl_1907596.smi 179: [09:08:38] done 179: [09:08:38] ------------------------------------- 179: [09:08:38] Test2 162: ........................................[09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: .[09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: .[09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: .[09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored 162: ................. 162: ---------------------------------------------------------------------- 162: Ran 60 tests in 11.213s 162: 162: OK 162/230 Test #162: pyFMCS ................................. Passed 11.77 sec test 182 Start 182: testRGroupDecomp 182: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 182: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 182: Test timeout computed to be: 1500 179: [09:08:39] done 179: [09:08:39] ------------------------------------- 179: [09:08:39] Test3 (stereo options) 163/230 Test #178: trajectoryTest ......................... Passed 1.26 sec test 183 Start 183: testRGroupDecompInternals 183: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 183: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 183: Test timeout computed to be: 1500 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 164/230 Test #183: testRGroupDecompInternals .............. Passed 0.10 sec test 184 Start 184: rgroupCatchTests 184: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 184: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 184: Test timeout computed to be: 1500 179: [09:08:39] Done (stereo options) 179: [09:08:39] ------------------------------------- 179: [09:08:39] Test4 (trusted smiles) 27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 179: [09:08:39] Done (trusted smiles) 179: [09:08:39] ------------------------------------- 179: [09:08:39] Testing C++ docs 179: [09:08:39] Done (C++ doc tests) 179: [09:08:39] ------------------------------------- 179: [09:08:39] Testing C++ ring query: PatternHolder 179: [09:08:39] Done (C++ ring query tests) 179: [09:08:39] ------------------------------------- 179: [09:08:39] Testing C++ ring query: TautomerPatternHolder 179: [09:08:39] Done (C++ ring query tests) 179: [09:08:39] ------------------------------------- 179: [09:08:39] Add Patterns 27: All 191 tests passed 27: 27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 182: [09:08:39] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters 182: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors 184: Randomness seeded to: 2922787517 184: =============================================================================== 184: All tests passed (1475 assertions in 14 test cases) 184: 165/230 Test #184: rgroupCatchTests ....................... Passed 0.55 sec test 185 Start 185: pyRGroupDecomposition 185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 185: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 185: Test timeout computed to be: 1500 180: Randomness seeded to: 310564961 180: =============================================================================== 180: All tests passed (171 assertions in 5 test cases) 180: 166/230 Test #180: substructLibraryCatchTest .............. Passed 1.71 sec test 186 Start 186: molInterchangeTest1 186: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 186: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 186: Test timeout computed to be: 1500 186: [09:08:39] test1: basics 186: [09:08:39] done 186: [09:08:39] test2: basic writing 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[0,0]}]}]} 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} 186: [09:08:39] done 186: [09:08:39] test3: writing conformers 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1987,-0.0452],[-0.3332,0.4555],[0.1659,1.322],[0.5332,-0.0438],[-2.0652,0.4541],[-0.8339,1.3212]]},{"dim":3,"coords":[[0.9553,-0.3743,-0.4679],[-0.3616,-0.131,-0.0794],[-0.5097,1.6255,0.1705],[-0.5778,-0.7919,1.1042],[1.5276,0.1063,0.1627],[-1.0339,-0.4345,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.2","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} 186: [09:08:39] done 186: [09:08:39] test4: writing properties 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[0,0]}]}]} 186: [09:08:39] done 186: [09:08:39] test5: writing partial charges 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.2","values":[0.5,-0.5]}]}]} 186: [09:08:39] testing parse options 186: [09:08:39] done 186: [09:08:39] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} 186: [09:08:39] done 186: [09:08:39] testing 'either' stereochemistry 186: [09:08:39] done 167/230 Test #186: molInterchangeTest1 .................... Passed 0.12 sec test 187 Start 187: molInterchangeCatchTest 187: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 187: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 187: Test timeout computed to be: 1500 157: Done 157: ----------------- Test Github #781: Rendering single-atom molecules 157: Done 157: ----------------- Test 3 187: Randomness seeded to: 3737209786 187: [09:08:40] unrecognized bond type 12 set to zero while writing 187: [09:08:40] unrecognized bond type 0 set to zero while writing 157: file test3_1.png gave hash 1514877476U not the expected 3984824963U 187: =============================================================================== 187: All tests passed (122 assertions in 6 test cases) 187: 168/230 Test #187: molInterchangeCatchTest ................ Passed 0.12 sec test 188 Start 188: pyMolInterchange 188: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 188: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 188: Test timeout computed to be: 1500 157: file test3_2.png gave hash 895995063U not the expected 238321316U 157: file test3_3.png gave hash 2806558077U not the expected 414888185U 157: file test3_4.png gave hash 3204576434U not the expected 2265825690U 157: file test3_5.png gave hash 3784843232U not the expected 1911551403U 168: Randomness seeded to: 1143299777 168: Timed out after 11 seconds. 157: file test3_6.png gave hash 2648864811U not the expected 577293879U 157: file test3_7.png gave hash 727952731U not the expected 248355372U 157: Done 157: ----------------- Test Github774: upside-down drawings 157: file test774_1.png gave hash 1746502640U not the expected 927423591U 157: file test774_2.png gave hash 1057482804U not the expected 1171827286U 157: Done 157: ----------------- Test 9 (molecule legends) 157: file test9_1.svg gave hash 923579170U not the expected 1484349178U 157: Done 157: ----------------- Test Github852: Lines used to wedge bonds are too thick 157: file test852_1.png gave hash 3083219870U not the expected 736085072U 157: file test852_2.png gave hash 1999141294U not the expected 1438089260U 157: ---------------- 157: ---------------- 157: ---------------- 157: ---------------- 157: Done 157: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right 157: file test860_1.png gave hash 667708706U not the expected 2065140854U 157: file test860_2.png gave hash 2350165565U not the expected 3098360765U 157: file test860_3.png gave hash 3798998670U not the expected 3439618110U 157: Done 157: ----------------- Test Github #910: ugly coordinates generated for peptide chains 157: Done 157: ----------------- Test Github #932: mistake in SVG for wedged bonds 157: Done 157: ----------------- Test Github #953: default color should not be cyan 157: Done 157: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly 157: Done 157: ----------------- Test Deuterium, Tritium 157: Done 157: ----------------- Test crossed bonds 157: Done 157: ----------------- Testing drawing a second molecule 157: Done 157: ----------------- Testing drawing a grid of molecules 157: Done 157: ----------------- Testing drawMolecules 157: file test12_1.svg gave hash 2982175789U not the expected 881731720U 157: Done 157: ----------------- Test JSON Configuration 157: Done 157: ----------------- Testing github 1090: escape html characters in SVG output 157: Done 157: ----------------- Testing github 1035: overflow bug in SVG color generation 157: Done 157: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes 157: Done 157: ----------------- Testing github 1322: add custom atom labels 157: Done 157: ----------------- Testing use of a black & white palette 157: Done 157: ----------------- Testing use of continuous highlighting with drawMolecules 157: Done 157: ----------------- Test 17 - Testing maximum font size 188: .. 188: ---------------------------------------------------------------------- 188: Ran 2 tests in 0.039s 188: 188: OK 157: Done 157: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list 157: Done 157: ----------------- Testing use of fixed scales for drawing. 157: Done 157: ----------------- Testing rotation of 2D drawing. 157: Done 157: ----------------- Testing inclusion of molecule metadata 157: Done 157: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default 157: Done 157: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions 157: file testGithub2151_1.svg gave hash 3620378781U not the expected 4119581143U 157: file testGithub2151_2.svg gave hash 3896781930U not the expected 425960913U 157: Done 157: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn 157: Done 157: ----------------- Testing testGithub2931: multi-coloured molecule highlights. 157: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U 157: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U 157: Done 157: ----------------- Testing annotation of 2D Drawing. 157: file test20_1.png gave hash 2978996523U not the expected 1672353490U 169/230 Test #188: pyMolInterchange ....................... Passed 1.42 sec test 189 Start 189: testSLNParse 189: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 189: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 189: Test timeout computed to be: 1500 157: file test20_2.png gave hash 745058850U not the expected 1073213605U 189: Atoms: 189: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 189: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 189: 2 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 189: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 189: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 189: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 189: Bonds: 189: 0 0->1 order: 1 189: 1 0->2 order: 1 189: 2 0->3 order: 1 189: 3 0->4 order: 1 189: 4 0->5 order: 1 189: [09:08:41] SLN Parse Error: syntax error while parsing: CH4[I=13] 189: [09:08:41] Failed parsing SLN 'CH4[I=13]' 189: [09:08:41] SLN Parser error: Atom ID 1 appears *after* its ring closure. 189: [09:08:41] SLN Parser error: Ring closure 1 does not have a corresponding opener. 189: [09:08:41] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) 189: [09:08:41] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' 189: [09:08:41] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) 189: [09:08:41] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' 189: [09:08:41] SLN Parse Error: syntax error while parsing: CH4 fff 189: [09:08:41] Failed parsing SLN 'CH4 fff' 189: [09:08:41] SLN Parse Error: syntax error while parsing: C[charge=+1] foo 189: [09:08:41] Failed parsing SLN 'C[charge=+1] foo' 189: [09:08:41] Query property 'is' ignored on non-query atom 189: [09:08:41] Query property 'is' ignored on non-query atom 170/230 Test #189: testSLNParse ........................... Passed 0.07 sec test 190 Start 190: pySLNParse 190: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/Wrap/testSLN.py" 190: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap 190: Test timeout computed to be: 1500 157: file test20_3.png gave hash 472521001U not the expected 471234756U 157: file test20_4.png gave hash 1015859242U not the expected 2803490234U 157: Done 157: ----------------- Test 21 - different font 157: Done 157: ----------------- Test 22 - draw explicit methyls. 157: Done 157: ----------------- Testing drawing of legends. 157: Done 157: ----------------- Test Github 3305 - change and scale line widths. 157: file testGithub3305_1.png gave hash 588173490U not the expected 1801411420U 157: file testGithub3305_2.png gave hash 3393765154U not the expected 2904846519U 157: file testGithub3305_3.png gave hash 694090236U not the expected 2915229647U 157: file testGithub3305_4.png gave hash 3784843232U not the expected 1911551403U 157: file testGithub3305_5.png gave hash 2382054754U not the expected 614319597U 157: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U 157: file testGithub3305_6.png gave hash 1247498295U not the expected 3926947401U 157: file testGithub3305_7.png gave hash 3628125988U not the expected 1720405002U 157: Done 157: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. 157: Done 157: ----------------- Test Github 4156 - bad scale for radicals in grid 157: Done 157: ----------------- Test JSON atomColourPalette 157: Done 157: ----------------- Test draw aromatic OR queries 157: Done 157: ----------------- Test AND queries 157: Done 171/230 Test #157: moldraw2DTest1 ......................... Passed 16.02 sec test 191 Start 191: pyGraphMolWrap 191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rough_test.py" 191: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 191: Test timeout computed to be: 1500 190: .. 190: ---------------------------------------------------------------------- 190: Ran 2 tests in 0.027s 190: 190: OK 172/230 Test #190: pySLNParse ............................. Passed 0.91 sec test 192 Start 192: pyTestConformerWrap 192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testConformer.py" 192: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 192: Test timeout computed to be: 1500 79: =============================================================================== 79: All tests passed (1586 assertions in 98 test cases) 79: 173/230 Test #79: fileParsersCatchTest ................... Passed 29.23 sec test 193 Start 193: pyTestTrajectory 193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testTrajectory.py" 193: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 193: Test timeout computed to be: 1500 191: ..............[09:08:43] SMARTS Parse Error: syntax error while parsing: fiib 191: [09:08:43] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' 191: ....[09:08:43] ERROR: Problems encountered parsing data fields 191: [09:08:43] ERROR: moving to the beginning of the next molecule 191: [09:08:43] ERROR: Problems encountered parsing data fields 191: [09:08:43] ERROR: moving to the beginning of the next molecule 191: [09:08:43] Spurious data before the first property will be ignored 191: [09:08:43] Property will be truncated after the first blank line 191: [09:08:43] Property will be truncated after the first blank line 191: [09:08:43] Property will be truncated after the first blank line 191: [09:08:43] ERROR: Problems encountered parsing data fields 191: [09:08:43] ERROR: moving to the beginning of the next molecule 191: [09:08:43] ERROR: Problems encountered parsing data fields 191: [09:08:43] ERROR: moving to the beginning of the next molecule 191: [09:08:43] Spurious data before the first property will be ignored 191: [09:08:43] Property will be truncated after the first blank line 191: [09:08:43] Property will be truncated after the first blank line 191: [09:08:43] Property will be truncated after the first blank line 191: [09:08:43] ERROR: Problems encountered parsing data fields 191: [09:08:43] ERROR: moving to the beginning of the next molecule 191: [09:08:43] Property will be truncated after the first blank line 191: [09:08:43] ERROR: Problems encountered parsing data fields 191: [09:08:43] ERROR: moving to the beginning of the next molecule 191: [09:08:43] Property will be truncated after the first blank line 191: .[09:08:43] SMILES Parse Error: syntax error while parsing: fail 191: [09:08:43] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 191: [09:08:43] ERROR: Smiles parse error on line 2 191: [09:08:43] ERROR: Cannot create molecule from : 'fail' 191: >>> This may result in an infinite loop. It should finish almost instantly 191: <<< OK, it finished. 191: ............[09:08:43] Explicit valence for atom # 1 C, 5, is greater than permitted 191: ......[09:08:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 191: [09:08:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 191: [09:08:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 191: [09:08:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 191: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| 192: ...... 192: ---------------------------------------------------------------------- 192: Ran 6 tests in 0.073s 192: 192: OK 191: ........[09:08:43] non-ring atom 0 marked aromatic 191: [09:08:43] non-ring atom 0 marked aromatic 191: [09:08:43] 191: 191: **** 191: Range Error 191: idx 191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 191: Failed Expression: 12 < 6 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 4# 0x00007F21EB47C4C0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 32# _PyObject_Call_Prepend in /usr/bin/python3 191: 33# 0x000000000059D6E4 in /usr/bin/python3 191: 34# _PyObject_MakeTpCall in /usr/bin/python3 191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 36# 0x0000000000546E76 in /usr/bin/python3 191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 38# _PyObject_Call_Prepend in /usr/bin/python3 191: 39# 0x000000000059D6E4 in /usr/bin/python3 191: 40# _PyObject_MakeTpCall in /usr/bin/python3 191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 42# 0x0000000000546E76 in /usr/bin/python3 191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 44# _PyObject_Call_Prepend in /usr/bin/python3 191: 45# 0x000000000059D6E4 in /usr/bin/python3 191: 46# _PyObject_MakeTpCall in /usr/bin/python3 191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 48# _PyObject_Call_Prepend in /usr/bin/python3 191: 49# 0x000000000059810D in /usr/bin/python3 191: 50# 0x0000000000593E22 in /usr/bin/python3 191: 51# _PyObject_MakeTpCall in /usr/bin/python3 191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 53# PyEval_EvalCode in /usr/bin/python3 191: 54# 0x00000000005FFE7F in /usr/bin/python3 191: 55# 0x00000000006A59F2 in /usr/bin/python3 191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: [09:08:43] non-ring atom 0 marked aromatic 191: [09:08:43] non-ring atom 0 marked aromatic 191: [09:08:43] 191: 191: **** 191: Range Error 191: idx 191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 191: Failed Expression: 12 < 6 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 4# 0x00007F21EB47C4C0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 32# _PyObject_Call_Prepend in /usr/bin/python3 191: 33# 0x000000000059D6E4 in /usr/bin/python3 191: 34# _PyObject_MakeTpCall in /usr/bin/python3 191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 36# 0x0000000000546E76 in /usr/bin/python3 191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 38# _PyObject_Call_Prepend in /usr/bin/python3 191: 39# 0x000000000059D6E4 in /usr/bin/python3 191: 40# _PyObject_MakeTpCall in /usr/bin/python3 191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 42# 0x0000000000546E76 in /usr/bin/python3 191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 44# _PyObject_Call_Prepend in /usr/bin/python3 191: 45# 0x000000000059D6E4 in /usr/bin/python3 191: 46# _PyObject_MakeTpCall in /usr/bin/python3 191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 48# _PyObject_Call_Prepend in /usr/bin/python3 191: 49# 0x000000000059810D in /usr/bin/python3 191: 50# 0x0000000000593E22 in /usr/bin/python3 191: 51# _PyObject_MakeTpCall in /usr/bin/python3 191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 53# PyEval_EvalCode in /usr/bin/python3 191: 54# 0x00000000005FFE7F in /usr/bin/python3 191: 55# 0x00000000006A59F2 in /usr/bin/python3 191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: ...............[09:08:43] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 191: [09:08:43] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 174/230 Test #192: pyTestConformerWrap .................... Passed 1.26 sec test 194 Start 194: pyTestSGroups 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testSGroups.py" 194: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 194: Test timeout computed to be: 1500 193: [09:08:43] 193: 193: **** 193: Pre-condition Violation 193: from must be < size() 193: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: from < static_cast(size()) 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: .[09:08:43] 193: 193: **** 193: Pre-condition Violation 193: from must be < size() 193: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: from < static_cast(size()) 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 191: ..............[09:08:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 191: [09:08:43] Explicit valence for atom # 1 C, 5, is greater than permitted 193: .[09:08:44] 193: 193: **** 193: Range Error 193: snapshotNum 193: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: 0 < 0 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x0000000000546E76 in /usr/bin/python3 193: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 27# _PyObject_Call_Prepend in /usr/bin/python3 193: 28# 0x000000000059D6E4 in /usr/bin/python3 193: 29# _PyObject_MakeTpCall in /usr/bin/python3 193: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 31# 0x0000000000546E76 in /usr/bin/python3 193: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 33# _PyObject_Call_Prepend in /usr/bin/python3 193: 34# 0x000000000059D6E4 in /usr/bin/python3 193: 35# _PyObject_MakeTpCall in /usr/bin/python3 193: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 37# 0x0000000000546E76 in /usr/bin/python3 193: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 39# _PyObject_Call_Prepend in /usr/bin/python3 193: 40# 0x000000000059D6E4 in /usr/bin/python3 193: 41# _PyObject_MakeTpCall in /usr/bin/python3 193: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 43# _PyObject_Call_Prepend in /usr/bin/python3 193: 44# 0x000000000059810D in /usr/bin/python3 193: 45# 0x0000000000593E22 in /usr/bin/python3 193: 46# _PyObject_MakeTpCall in /usr/bin/python3 193: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 48# PyEval_EvalCode in /usr/bin/python3 193: 49# 0x00000000005FFE7F in /usr/bin/python3 193: 50# 0x00000000006A59F2 in /usr/bin/python3 193: 51# _PyRun_SimpleFileObject in /usr/bin/python3 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 193: 55# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: .[09:08:44] 193: 193: **** 193: Pre-condition Violation 193: The trajectory must have dimension == 3 193: Violation occurred on line 113 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: traj.dimension() == 3 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: ..[09:08:44] 193: 193: **** 193: Pre-condition Violation 193: The trajectory must have dimension == 3 193: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: traj.dimension() == 3 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: .[09:08:44] 193: 193: **** 193: Pre-condition Violation 193: d_pos must not be NULL 193: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: d_pos 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: [09:08:44] 193: 193: **** 193: Pre-condition Violation 193: d_trajectory must not be NULL 193: Violation occurred on line 24 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: d_trajectory 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: .[09:08:44] 193: 193: **** 193: Range Error 193: snapshotNum 193: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: 5 < 5 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x0000000000546E76 in /usr/bin/python3 193: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 27# _PyObject_Call_Prepend in /usr/bin/python3 193: 28# 0x000000000059D6E4 in /usr/bin/python3 193: 29# _PyObject_MakeTpCall in /usr/bin/python3 193: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 31# 0x0000000000546E76 in /usr/bin/python3 193: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 33# _PyObject_Call_Prepend in /usr/bin/python3 193: 34# 0x000000000059D6E4 in /usr/bin/python3 193: 35# _PyObject_MakeTpCall in /usr/bin/python3 193: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 37# 0x0000000000546E76 in /usr/bin/python3 193: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 39# _PyObject_Call_Prepend in /usr/bin/python3 193: 40# 0x000000000059D6E4 in /usr/bin/python3 193: 41# _PyObject_MakeTpCall in /usr/bin/python3 193: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 43# _PyObject_Call_Prepend in /usr/bin/python3 193: 44# 0x000000000059810D in /usr/bin/python3 193: 45# 0x0000000000593E22 in /usr/bin/python3 193: 46# _PyObject_MakeTpCall in /usr/bin/python3 193: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 48# PyEval_EvalCode in /usr/bin/python3 193: 49# 0x00000000005FFE7F in /usr/bin/python3 193: 50# 0x00000000006A59F2 in /usr/bin/python3 193: 51# _PyRun_SimpleFileObject in /usr/bin/python3 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 193: 55# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: [09:08:44] 193: 193: **** 193: Range Error 193: pointNum 193: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: 10 < 10 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: .[09:08:44] 193: 193: **** 193: Range Error 193: snapshotNum 193: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: 5 < 5 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x0000000000546E76 in /usr/bin/python3 193: 26# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 27# _PyObject_Call_Prepend in /usr/bin/python3 193: 28# 0x000000000059D6E4 in /usr/bin/python3 193: 29# _PyObject_MakeTpCall in /usr/bin/python3 193: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 31# 0x0000000000546E76 in /usr/bin/python3 193: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 33# _PyObject_Call_Prepend in /usr/bin/python3 193: 34# 0x000000000059D6E4 in /usr/bin/python3 193: 35# _PyObject_MakeTpCall in /usr/bin/python3 193: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 37# 0x0000000000546E76 in /usr/bin/python3 193: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 39# _PyObject_Call_Prepend in /usr/bin/python3 193: 40# 0x000000000059D6E4 in /usr/bin/python3 193: 41# _PyObject_MakeTpCall in /usr/bin/python3 193: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 43# _PyObject_Call_Prepend in /usr/bin/python3 193: 44# 0x000000000059810D in /usr/bin/python3 193: 45# 0x0000000000593E22 in /usr/bin/python3 193: 46# _PyObject_MakeTpCall in /usr/bin/python3 193: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 48# PyEval_EvalCode in /usr/bin/python3 193: 49# 0x00000000005FFE7F in /usr/bin/python3 193: 50# 0x00000000006A59F2 in /usr/bin/python3 193: 51# _PyRun_SimpleFileObject in /usr/bin/python3 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 193: 55# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: [09:08:44] 193: 193: **** 193: Pre-condition Violation 193: d_dimension must be == 2 193: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: d_trajectory->dimension() == 2 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: [09:08:44] 193: 193: **** 193: Pre-condition Violation 193: d_dimension must be == 2 193: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 193: Failed Expression: d_trajectory->dimension() == 2 193: ---------- 193: Stacktrace: 193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 26# _PyObject_Call_Prepend in /usr/bin/python3 193: 27# 0x000000000059D6E4 in /usr/bin/python3 193: 28# _PyObject_MakeTpCall in /usr/bin/python3 193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 30# 0x0000000000546E76 in /usr/bin/python3 193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 32# _PyObject_Call_Prepend in /usr/bin/python3 193: 33# 0x000000000059D6E4 in /usr/bin/python3 193: 34# _PyObject_MakeTpCall in /usr/bin/python3 193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 36# 0x0000000000546E76 in /usr/bin/python3 193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 38# _PyObject_Call_Prepend in /usr/bin/python3 193: 39# 0x000000000059D6E4 in /usr/bin/python3 193: 40# _PyObject_MakeTpCall in /usr/bin/python3 193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 42# _PyObject_Call_Prepend in /usr/bin/python3 193: 43# 0x000000000059810D in /usr/bin/python3 193: 44# 0x0000000000593E22 in /usr/bin/python3 193: 45# _PyObject_MakeTpCall in /usr/bin/python3 193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 47# PyEval_EvalCode in /usr/bin/python3 193: 48# 0x00000000005FFE7F in /usr/bin/python3 193: 49# 0x00000000006A59F2 in /usr/bin/python3 193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: 193: . 193: ---------------------------------------------------------------------- 193: Ran 9 tests in 0.637s 193: 193: OK 193: Testing Trajectory wrapper 185: .................... 185: ---------------------------------------------------------------------- 185: Ran 20 tests in 4.025s 185: 185: OK 175/230 Test #193: pyTestTrajectory ....................... Passed 1.29 sec test 195 Start 195: pyTestThreads 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testThreads.py" 195: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 191: ............................[09:08:44] unable to set wavy bonds for double bonds: 3 176/230 Test #185: pyRGroupDecomposition .................. Passed 5.14 sec test 196 Start 196: pyTestMultithreadedMolSupplier 196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 196: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 196: Test timeout computed to be: 1500 191: .............[09:08:45] 191: 191: **** 191: Range Error 191: idx 191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 191: Failed Expression: 6 < 5 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 32# _PyObject_Call_Prepend in /usr/bin/python3 191: 33# 0x000000000059D6E4 in /usr/bin/python3 191: 34# _PyObject_MakeTpCall in /usr/bin/python3 191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 36# 0x0000000000546E76 in /usr/bin/python3 191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 38# _PyObject_Call_Prepend in /usr/bin/python3 191: 39# 0x000000000059D6E4 in /usr/bin/python3 191: 40# _PyObject_MakeTpCall in /usr/bin/python3 191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 42# 0x0000000000546E76 in /usr/bin/python3 191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 44# _PyObject_Call_Prepend in /usr/bin/python3 191: 45# 0x000000000059D6E4 in /usr/bin/python3 191: 46# _PyObject_MakeTpCall in /usr/bin/python3 191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 48# _PyObject_Call_Prepend in /usr/bin/python3 191: 49# 0x000000000059810D in /usr/bin/python3 191: 50# 0x0000000000593E22 in /usr/bin/python3 191: 51# _PyObject_MakeTpCall in /usr/bin/python3 191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 53# PyEval_EvalCode in /usr/bin/python3 191: 54# 0x00000000005FFE7F in /usr/bin/python3 191: 55# 0x00000000006A59F2 in /usr/bin/python3 191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: 194: ............. 194: ---------------------------------------------------------------------- 194: Ran 13 tests in 0.138s 194: 194: OK 194: Testing SubstanceGroups wrapper 50: Randomness seeded to: 860647536 50: =============================================================================== 50: All tests passed (14835 assertions in 14 test cases) 50: 177/230 Test #50: canonTestsCatch ........................ Passed 31.97 sec test 197 Start 197: pyTestPropertyLists 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testPropertyLists.py" 197: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 178/230 Test #194: pyTestSGroups .......................... Passed 1.73 sec test 198 Start 198: pyCDXMLTest 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/test_cdxml.py" 198: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 196: .s. 196: ---------------------------------------------------------------------- 196: Ran 3 tests in 0.442s 196: 196: OK (skipped=1) 196: Testing Smiles and SD MultithreadedMolSupplier 197: [09:08:46] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 197: [09:08:46] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 197: [09:08:46] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 197: .[09:08:46] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 197: [09:08:46] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 197: [09:08:46] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 197: ...[09:08:46] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 197: [09:08:46] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 197: [09:08:46] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 197: . 197: ---------------------------------------------------------------------- 197: Ran 5 tests in 0.017s 197: 197: OK 179/230 Test #197: pyTestPropertyLists .................... Passed 0.97 sec test 199 Start 199: molStandardizeTest 199: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 199: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 199: Test timeout computed to be: 1500 180/230 Test #196: pyTestMultithreadedMolSupplier ......... Passed 1.46 sec test 200 Start 200: molNormalizeTest 200: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 200: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 200: Test timeout computed to be: 1500 198: . 198: ---------------------------------------------------------------------- 198: Ran 1 test in 0.033s 198: 198: OK 200: [09:08:46] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 182: iterative 179: [09:08:46] ------------------------------------- 179: [09:08:46] testing PatternHolder 181/230 Test #198: pyCDXMLTest ............................ Passed 1.37 sec test 201 Start 201: molValidateTest 201: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 201: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 201: Test timeout computed to be: 1500 200: [09:08:46] Initializing Normalizer 200: [09:08:46] Running Normalizer 200: [09:08:46] Rule applied: BrokenazidetoN=N+=N- 200: [09:08:46] Initializing Normalizer 200: [09:08:46] Running Normalizer 200: [09:08:46] Initializing Normalizer 200: [09:08:46] Running Normalizer 182/230 Test #200: molNormalizeTest ....................... Passed 0.62 sec test 202 Start 202: molChargeTest 202: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 202: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 202: Test timeout computed to be: 1500 150: .............[09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 201: ERROR: [FeaturesValidation] Query atom 0 is not allowed 201: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed 201: ERROR: [FeaturesValidation] Query bond 0 is not allowed 201: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed 201: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed 201: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed 201: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed 201: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed 201: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed 201: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed 201: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed 201: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed 201: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed 201: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. 201: here 201: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 201: there 201: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. 183/230 Test #202: molChargeTest .......................... Passed 0.13 sec test 203 Start 203: molTautomerTest 203: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 203: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 203: Test timeout computed to be: 1500 179: [09:08:47] ------------------------------------- 179: [09:08:47] testing TautomerPatternHolder 184/230 Test #201: molValidateTest ........................ Passed 0.24 sec test 204 Start 204: molStandardizeSmallTest 204: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 204: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 204: Test timeout computed to be: 1500 185/230 Test #204: molStandardizeSmallTest ................ Passed 0.08 sec test 205 Start 205: molFragmentTest 205: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 205: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 205: Test timeout computed to be: 1500 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 191: ....................[09:08:47] Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:47] Explicit valence for atom # 6 F, 2, is greater than permitted 191: [09:08:47] Can't kekulize mol. Unkekulized atoms: 3 4 5 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 205: [09:08:47] SMARTS Parse Error: syntax error while parsing: [Cl 205: [09:08:47] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 186/230 Test #205: molFragmentTest ........................ Passed 0.09 sec test 206 Start 206: molStandardizeCatchTest 206: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 206: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 179: [09:08:47] ------------------------------------- 179: [09:08:47] testSegFaultInHolder 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error[09:08:47] SMILES Parse Error: syntax error[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: syntax error[09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[09:08:47] dsafsdfSMILES Parse Error: syntax error while parsing: '[09:08:47] 179: SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: dsafsdf 179: while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: while parsing: dsafsdf[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:08:47] dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] [09:08:47] [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: while parsing: dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: ' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: 179: [09:08:47] [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: SMILES Parse Error: syntax error while parsing: dsafsdf 179: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: [09:08:47] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf 179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: [09:08:47] ------------------------------------- 179: [09:08:47] Results do not depend on numThreads 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() 191: .................[09:08:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 187/230 Test #199: molStandardizeTest ..................... Passed 2.04 sec test 207 Start 207: molStandardizePipelineTest 207: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 207: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 207: Randomness seeded to: 1316290529 207: 1 Counts line too short: '' on line4 207: 1 Could not instantiate a valid molecule from input 207: 8 Molecule has no atoms 207: [09:08:48] Explicit valence for atom # 1 N, 4, is greater than permitted 207: [09:08:48] Explicit valence for atom # 1 N, 4, is greater than permitted 207: 8 Explicit valence for atom # 1 N, 4, is greater than permitted 207: 128 An error occurred while preparing the molecule for standardization. 207: 8 The molecule contains an unknown isotope: 3C 207: 4 Query atom 0 is not allowed 207: 4 Bond 0 of aromatic type is not allowed 207: 4 Bond 1 of aromatic type is not allowed 207: 4 Bond 2 of aromatic type is not allowed 207: 4 Bond 3 of aromatic type is not allowed 207: 4 Bond 5 of aromatic type is not allowed 207: 4 Bond 6 of aromatic type is not allowed 207: 4 Bond 2 of dative type is not allowed 207: 4 Bond 3 of dative type is not allowed 207: 4 Enhanced stereochemistry features are not allowed 207: 8 The radical at atom 0 is not allowed 207: [09:08:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 207: 16 The molecule includes non-null Z coordinates 207: 32 Atom 0 too close to bond 2 207: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit 207: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds 207: 64 Atom 0 has adjacent stereo bonds with like orientation 207: [09:08:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 207: 16 The molecule includes non-null Z coordinates 207: 64 Atom 0 has adjacent stereo bonds with like orientation 206: Randomness seeded to: 1025550055 206: * - * - * - * m1 207: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit 207: 8388608 One or more metal atoms were disconnected. 207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 207: 67108864 The protonation state was adjusted. 206: * - * - * - * m2 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. 207: 16777216 The representation of some functional groups was adjusted. 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. 206: * - * - * - * m1 206: * - * - * - * m2 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. 182: bulk 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. 207: 8388608 One or more metal atoms were disconnected. 207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 207: 67108864 The protonation state was adjusted. 206: [09:08:48] Can't kekulize mol. Unkekulized atoms: 3 7 207: 8388608 One or more metal atoms were disconnected. 207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 207: 67108864 The protonation state was adjusted. 207: 8388608 One or more metal atoms were disconnected. 207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 207: 67108864 The protonation state was adjusted. 207: 8388608 One or more metal atoms were disconnected. 207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 207: 67108864 The protonation state was adjusted. 206: [09:08:48] Can't kekulize mol. Unkekulized atoms: 3 8 207: 8388608 One or more metal atoms were disconnected. 207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 207: 67108864 The protonation state was adjusted. 207: 16777216 The "wavy" style of bond 4 was removed 206: [09:08:48] Can't kekulize mol. Unkekulized atoms: 2 3 4 207: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 2 was removed 207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 1 was removed 207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 1 was removed 207: 16777216 The "wavy" style of bond 4 was removed 207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 3 was removed 207: 16777216 The representation of some functional groups was adjusted. 207: [09:08:48] Can't kekulize mol. Unkekulized atoms: 2 3 5 207: =============================================================================== 207: All tests passed (268 assertions in 5 test cases) 207: 188/230 Test #207: molStandardizePipelineTest ............. Passed 0.29 sec test 208 Start 208: pyMolStandardize 208: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 208: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 208: Test timeout computed to be: 1500 203: [09:08:48] Tautomer enumeration stopped at 292 tautomers: max transforms reached 203: [09:08:49] Tautomer enumeration stopped at 292 tautomers: max transforms reached 208: .....[09:08:49] Tautomer enumeration stopped at 292 tautomers: max transforms reached 203: [09:08:49] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 208: [09:08:49] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 208: .[09:08:50] Tautomer enumeration stopped at 25 tautomers: canceled 208: Enumeration was canceled due to timeout (50 ms) 203: [09:08:50] Tautomer enumeration stopped at 32 tautomers: canceled 203: Enumeration was canceled due to timeout (50 ms) 182: bulk, no symmetry 203: 375 203: Enumeration has completed 182: [09:08:52] Relabelling existing label 203: [09:08:52] Tautomer enumeration stopped at 67 tautomers: canceled 150: ...[09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() 150: [09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() 150: [09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() 150: [09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() 150: [09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() 173: VS001: PASSED 173: VS002: PASSED 173: VS003: PASSED 173: VS004: PASSED 173: VS005: PASSED 173: VS006: PASSED 173: VS007: PASSED 173: VS008: PASSED 173: VS009: PASSED 173: VS010: PASSED 173: VS011: PASSED 173: VS012: PASSED 173: VS013: PASSED 173: VS014: PASSED 173: VS015: PASSED 173: VS016: PASSED 173: VS017: PASSED 173: VS018: PASSED 173: VS019: PASSED 173: VS020: PASSED 173: VS021: PASSED 173: VS022: PASSED 173: VS023: PASSED 173: VS024: PASSED 173: VS025: PASSED 173: VS026: PASSED 173: VS027: PASSED 173: VS028: PASSED 173: VS029: PASSED 173: VS030: PASSED 173: VS031: PASSED 173: VS032: PASSED 173: VS033: PASSED 173: VS034: PASSED 173: VS035: PASSED 173: VS036: PASSED 173: VS037: PASSED 173: VS038: PASSED 173: VS039: PASSED 173: VS040: PASSED 173: VS041: PASSED 173: VS042: PASSED 173: VS043: PASSED 173: VS044: PASSED 173: VS045: PASSED 173: VS046: PASSED 173: VS047: PASSED 173: VS048: PASSED 173: VS049: PASSED 173: VS050: PASSED 173: VS051: PASSED 173: VS052: PASSED 173: VS053: PASSED 173: VS054: PASSED 173: VS055: PASSED 173: VS056: PASSED 173: VS057: PASSED 173: VS058: PASSED 173: VS059: PASSED 173: VS060: PASSED 173: VS061: PASSED 173: VS062: PASSED 173: VS063: PASSED 173: VS064: PASSED 173: VS065: PASSED 173: VS066: PASSED 173: VS067: PASSED 173: VS068: PASSED 173: VS069: PASSED 173: VS070: PASSED 173: VS071: PASSED 173: VS072: PASSED 173: VS073: PASSED 173: VS074: PASSED 173: VS075: PASSED 173: VS076: PASSED 173: VS077: PASSED 173: VS078: PASSED 173: VS079: PASSED 173: VS080: PASSED 173: VS081: PASSED 173: VS082: PASSED 173: VS083: PASSED 173: VS084: PASSED 173: VS085: PASSED 173: VS086: PASSED 173: VS087: PASSED 173: VS088: PASSED 173: VS089: PASSED 173: VS090: PASSED 173: VS091: PASSED 173: VS092: PASSED 173: VS093: PASSED 173: VS094: PASSED 173: VS095: PASSED 173: VS096: PASSED 173: VS097: PASSED 173: VS098: PASSED 173: VS099: PASSED 173: VS100: PASSED 173: VS101: PASSED 173: VS102: PASSED 173: VS103: PASSED 173: VS104: PASSED 173: VS105: PASSED 173: VS106: PASSED 173: VS107: PASSED 173: VS108: PASSED 173: VS109: PASSED 173: VS110: PASSED 173: VS111: PASSED 173: VS112: PASSED 173: VS113: PASSED 173: VS114: PASSED 173: VS115: PASSED 173: VS116: PASSED 173: VS117: PASSED 173: VS118: PASSED 173: VS119: PASSED 173: VS120: PASSED 173: VS121: PASSED 173: VS122: PASSED 173: VS123: PASSED 173: VS124: PASSED 173: VS125: PASSED 173: VS126: PASSED 173: VS127: PASSED 173: VS128: PASSED 173: VS129: PASSED 173: VS130: PASSED 173: VS131: PASSED 173: VS132: PASSED 173: VS133: PASSED 173: VS134: PASSED 173: VS135: PASSED 173: VS136: PASSED 173: VS137: PASSED 173: VS138: PASSED 173: VS139: PASSED 173: VS140: PASSED 173: VS141: PASSED 173: VS142: PASSED 173: VS143: PASSED 173: VS144: PASSED 173: VS145: PASSED 173: VS146: PASSED 173: VS147: PASSED 173: VS148: PASSED 173: VS149: PASSED 173: VS150: PASSED 173: VS151: PASSED 173: VS152: PASSED 173: VS153: PASSED 173: VS154: PASSED 173: VS155: PASSED 173: VS156: PASSED 173: VS157: PASSED 173: VS158: PASSED 173: VS159: PASSED 173: VS160: PASSED 173: VS161: PASSED 173: VS162: PASSED 173: VS163: PASSED 173: VS164: PASSED 173: VS165: PASSED 173: VS166: PASSED 173: VS167: PASSED 173: VS168: PASSED 173: VS169: PASSED 173: VS170: PASSED 173: VS171: PASSED 173: VS172: PASSED 173: VS173: PASSED 173: VS174: PASSED 173: VS175: PASSED 173: VS176: PASSED 173: VS177: PASSED 173: VS178: PASSED 173: VS179: PASSED 173: VS180: PASSED 173: VS181: PASSED 173: VS182: PASSED 173: VS183: PASSED 173: VS184: PASSED 173: VS185: PASSED 173: VS186: PASSED 173: VS187: PASSED 173: VS188: PASSED 173: VS189: PASSED 173: VS190: PASSED 173: VS191: PASSED 173: VS192: PASSED 173: VS193: PASSED 173: VS194: PASSED 173: VS195: PASSED 173: VS196: PASSED 173: VS197: PASSED 173: VS198: PASSED 173: VS199: PASSED 173: VS200: PASSED 173: VS201: PASSED 173: VS202: PASSED 173: VS203: PASSED 173: VS204: PASSED 173: VS205: PASSED 173: VS206: PASSED 173: VS207: PASSED 173: VS208: PASSED 173: VS209: PASSED 173: VS210: PASSED 173: VS211: PASSED 173: VS212: PASSED 173: VS213: PASSED 173: VS214: PASSED 173: VS215: PASSED 173: VS216: PASSED 173: VS217: PASSED 173: VS218: PASSED 173: VS219: PASSED 173: VS220: PASSED 173: VS221: PASSED 173: VS222: PASSED 173: VS223: PASSED 173: VS224: PASSED 173: VS225: PASSED 173: VS226: PASSED 173: VS227: PASSED 173: VS228: PASSED 173: VS229: PASSED 173: VS230: PASSED 173: VS231: PASSED 173: VS232: PASSED 173: VS233: PASSED 173: VS234: PASSED 173: VS235: PASSED 173: VS236: PASSED 173: VS237: PASSED 173: VS238: PASSED 173: VS239: PASSED 173: VS240: PASSED 173: VS241: PASSED 173: VS242: PASSED 173: VS243: PASSED 173: VS244: PASSED 173: VS245: PASSED 173: VS246: PASSED 173: VS247: PASSED 173: VS248: PASSED 173: VS249: PASSED 173: VS250: PASSED 173: VS251: PASSED 173: VS252: PASSED 173: VS253: PASSED 173: VS254: PASSED 173: VS255: PASSED 173: VS256: PASSED 173: VS257: PASSED 173: VS258: PASSED 173: VS259: PASSED 173: VS260: PASSED 173: VS261: PASSED 173: VS262: PASSED 173: VS263: PASSED 173: VS264: PASSED 173: VS265: PASSED 173: VS266: PASSED 173: VS267: PASSED 173: VS268: PASSED 173: VS269: PASSED 173: VS270: PASSED 173: VS271: PASSED 173: VS272: PASSED 173: VS273: PASSED 173: VS274: PASSED 173: VS275: PASSED 173: VS276: PASSED 173: VS277: PASSED 173: VS278: PASSED 173: VS279: PASSED 173: VS280: PASSED 173: VS281: PASSED 173: VS282: PASSED 173: VS283: PASSED 173: VS284: PASSED 173: VS285: PASSED 173: VS286: PASSED 173: VS287: PASSED 173: VS288: PASSED 173: VS289: PASSED 173: VS290: PASSED 173: VS291: PASSED 173: VS292: PASSED 173: VS293: PASSED 173: VS294: PASSED 173: VS295: PASSED 173: VS296: PASSED 173: VS297: PASSED 173: VS298: PASSED 173: VS299: PASSED 173: VS300: PASSED 173: Check finished: 0 molecules failed. 173: Failed: 182: Best mapping 189/230 Test #173: pyCIPLabelsValidation .................. Passed 16.83 sec test 209 Start 209: testScaffoldNetwork 209: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 209: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork 209: Test timeout computed to be: 1500 150: ... 150: ---------------------------------------------------------------------- 150: Ran 19 tests in 28.907s 150: 150: OK 150: Testing MolAlign Wrappers 190/230 Test #150: pyMolAlign ............................. Passed 29.89 sec test 210 Start 210: pyScaffoldNetwork 210: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 210: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 210: Test timeout computed to be: 1500 208: Enumeration has completed 191/230 Test #182: testRGroupDecomp ....................... Passed 13.91 sec test 211 Start 211: pyScaffoldNetworkPickling 211: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 211: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 211: Test timeout computed to be: 1500 208: [09:08:53] Tautomer enumeration stopped at 42 tautomers: canceled 208: ..........[09:08:53] Explicit valence for atom # 1 N, 4, is greater than permitted 208: [09:08:53] Explicit valence for atom # 1 N, 4, is greater than permitted 208: [09:08:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 208: [09:08:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 179: [09:08:53] ------------------------------------- 179: [09:08:53] Results do not depend on numThreads (all same) 179: [09:08:53] ------------------------------------- 179: [09:08:53] testTautomerQueries 179: [09:08:53] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... 179: [09:08:53] ------------------------------------- 179: [09:08:53] github3881 recursive smarts with rings 192/230 Test #179: substructLibraryTest ................... Passed 15.85 sec test 212 Start 212: testMolEnumerator 212: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 212: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator 212: Test timeout computed to be: 1500 211: . 211: ---------------------------------------------------------------------- 211: Ran 1 test in 0.053s 211: 211: OK 212: Randomness seeded to: 2948331540 212: [09:08:54] can only enumerate SRUs with CONNECT=HT or CONNECT=HH 210: ....... 210: ---------------------------------------------------------------------- 210: Ran 7 tests in 0.104s 210: 210: OK 203: CN=c1cc[nH]cn1 203: CN=c1ccnc[nH]1 203: CNc1ccncn1 203: res: CNc1ccncn1 203: CN=c1cccc[nH]1 203: CNc1ccccn1 203: res: CNc1ccccn1 212: =============================================================================== 212: All tests passed (321 assertions in 16 test cases) 212: 193/230 Test #212: testMolEnumerator ...................... Passed 0.12 sec test 213 Start 213: pyMolEnumerator 213: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 213: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 213: Test timeout computed to be: 1500 194/230 Test #210: pyScaffoldNetwork ...................... Passed 1.30 sec test 214 Start 214: testAbbreviations 214: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 214: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations 214: Test timeout computed to be: 1500 214: Randomness seeded to: 4263323965 214: [09:08:54] SMARTS Parse Error: syntax error while parsing: *fail 214: [09:08:54] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' 195/230 Test #211: pyScaffoldNetworkPickling .............. Passed 1.32 sec test 215 Start 215: pyAbbreviations 215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 215: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 215: Test timeout computed to be: 1500 214: [09:08:54] no suitable SubstanceGroups found 214: =============================================================================== 214: All tests passed (195 assertions in 12 test cases) 214: 213: ... 213: ---------------------------------------------------------------------- 213: Ran 3 tests in 0.019s 213: 213: OK 196/230 Test #203: molTautomerTest ........................ Passed 7.32 sec 197/230 Test #214: testAbbreviations ...................... Passed 0.36 sec test 216 Start 216: generalizedSubstructCatch 216: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 216: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 216: Test timeout computed to be: 1500 test 217 Start 217: pyGeneralizedSubstruct 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 217: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 217: Test timeout computed to be: 1500 198/230 Test #213: pyMolEnumerator ........................ Passed 0.54 sec test 218 Start 218: testMolProcessing 218: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 218: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing 218: Test timeout computed to be: 1500 216: Randomness seeded to: 655562480 216: =============================================================================== 216: All tests passed (486 assertions in 10 test cases) 216: 199/230 Test #216: generalizedSubstructCatch .............. Passed 0.39 sec test 219 Start 219: pyMolProcessing 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 219: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 219: Test timeout computed to be: 1500 209: Randomness seeded to: 1616884633 209: =============================================================================== 209: All tests passed (269 assertions in 19 test cases) 209: 200/230 Test #209: testScaffoldNetwork .................... Passed 2.27 sec test 220 Start 220: testQuery 220: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Query/testQuery 220: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Query 220: Test timeout computed to be: 1500 220: Query 220: Query2 220: Equality 220: Greater 220: GreaterEqual 220: Less 220: LessEqual 220: Open Range 220: Closed Range 220: Float 220: With Tolerance 220: Set 220: And 220: Or 220: XOr 220: pointer and copy foo 220: Set2 201/230 Test #220: testQuery .............................. Passed 0.01 sec test 221 Start 221: testMatCalc 221: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 221: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc 221: Test timeout computed to be: 1500 221: 1.68022e+08 221: 1.73149e+08 221: 1.05549e+08 221: 7.20603e+07 221: 1.41535e+08 221: 1.08592e+08 221: 1.11334e+08 221: 2.05553e+08 221: 1.54962e+08 221: 8.08231e+07 221: 5.61421e+07 221: 1.28874e+08 221: 1.59011e+08 221: 8.69902e+07 221: 1.31367e+08 221: 2.27389e+08 221: 1.60289e+08 221: 7.79813e+07 221: 1.61001e+08 221: 2.07599e+08 221: 2.24432e+08 221: 1.39725e+08 221: 2.42614e+08 221: 1.77578e+08 221: 1.05908e+08 221: 9.06742e+07 221: 1.8087e+08 221: 1.98182e+08 221: 2.03052e+08 221: 1.7673e+08 221: 9.32798e+07 221: 1.37969e+08 221: 1.83778e+08 221: 2.1228e+08 221: 5.06157e+07 221: 1.566e+08 221: 2.37142e+08 221: 1.49345e+08 221: 7.05819e+07 221: 1.71633e+08 221: 1.96817e+08 221: 2.18246e+08 221: 9.49496e+07 221: 2.25618e+08 221: 1.30219e+08 202/230 Test #221: testMatCalc ............................ Passed 0.01 sec test 222 Start 222: pyMatCalc 222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 222: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 222: Test timeout computed to be: 1500 215: ....... 215: ---------------------------------------------------------------------- 215: Ran 7 tests in 0.026s 215: 215: OK 203/230 Test #215: pyAbbreviations ........................ Passed 0.85 sec test 223 Start 223: testSimDivPickers 223: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers 223: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers 223: Test timeout computed to be: 1500 223: [09:08:55] ------------------------------------- 223: [09:08:55] Testing github issue 1421: MaxMinPicker picking non-existent element. 223: [09:08:55] Done 223: [09:08:55] ------------------------------------- 223: [09:08:55] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. 223: [09:08:55] Done 204/230 Test #223: testSimDivPickers ...................... Passed 0.03 sec test 224 Start 224: pickersTestsCatch 224: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 224: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers 224: Test timeout computed to be: 1500 217: ....... 217: ---------------------------------------------------------------------- 217: Ran 7 tests in 0.233s 217: 217: OK 205/230 Test #217: pyGeneralizedSubstruct ................. Passed 1.07 sec test 225 Start 225: pySimDivPickers 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/testPickers.py" 225: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap 225: Test timeout computed to be: 1500 208: ............[09:08:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 208: [09:08:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 208: [09:08:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 224: Randomness seeded to: 1181784601 224: =============================================================================== 224: All tests passed (21267 assertions in 1 test case) 224: 206/230 Test #224: pickersTestsCatch ...................... Passed 0.24 sec test 226 Start 226: pyRanker 226: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/Wrap/testRanker.py" 226: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap 226: Test timeout computed to be: 1500 222: ..... 222: ---------------------------------------------------------------------- 222: Ran 5 tests in 0.429s 222: 222: OK 208: ........[09:08:56] Explicit valence for atom # 1 O, 3, is greater than permitted 208: . 208: ---------------------------------------------------------------------- 208: Ran 37 tests in 7.060s 208: 208: OK 208: done 161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 161: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 161: TOTAL Time elapsed 29.27 seconds 207/230 Test #161: testFMCS ............................... Passed 29.35 sec test 227 Start 227: testChemicalFeatures 227: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 227: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures 227: Test timeout computed to be: 1500 226: ..[09:08:56] 226: 226: **** 226: Invariant Violation 226: Can't rank more bits than the ensemble size 226: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp 226: Failed Expression: num <= dp_maskBits->getNumOnBits() 226: ---------- 226: Stacktrace: 226: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 226: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 226: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitInfoTheory.so.1 226: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 226: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 226: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 226: 6# 0x00007F89A78F362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 226: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 226: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 226: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 226: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 226: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 226: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 226: 13# 0x00007F89A78F03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 226: 14# _PyObject_MakeTpCall in /usr/bin/python3 226: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 16# 0x0000000000546E76 in /usr/bin/python3 226: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 18# _PyObject_Call_Prepend in /usr/bin/python3 226: 19# 0x000000000059D6E4 in /usr/bin/python3 226: 20# _PyObject_MakeTpCall in /usr/bin/python3 226: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 22# 0x0000000000546E76 in /usr/bin/python3 226: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 24# _PyObject_Call_Prepend in /usr/bin/python3 226: 25# 0x000000000059D6E4 in /usr/bin/python3 226: 26# _PyObject_MakeTpCall in /usr/bin/python3 226: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 28# 0x0000000000546E76 in /usr/bin/python3 226: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 30# _PyObject_Call_Prepend in /usr/bin/python3 226: 31# 0x000000000059D6E4 in /usr/bin/python3 226: 32# _PyObject_MakeTpCall in /usr/bin/python3 226: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 34# _PyObject_Call_Prepend in /usr/bin/python3 226: 35# 0x000000000059810D in /usr/bin/python3 226: 36# 0x0000000000593E22 in /usr/bin/python3 226: 37# _PyObject_MakeTpCall in /usr/bin/python3 226: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 39# PyEval_EvalCode in /usr/bin/python3 226: 40# 0x00000000005FFE7F in /usr/bin/python3 226: 41# 0x00000000006A59F2 in /usr/bin/python3 226: 42# _PyRun_SimpleFileObject in /usr/bin/python3 226: 43# _PyRun_AnyFileObject in /usr/bin/python3 226: 44# Py_RunMain in /usr/bin/python3 226: 45# Py_BytesMain in /usr/bin/python3 226: 46# 0x00007F89AA159D68 in /lib/x86_64-linux-gnu/libc.so.6 226: 47# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 226: 48# _start in /usr/bin/python3 226: ---------- 226: **** 226: 226: ... 226: ---------------------------------------------------------------------- 226: Ran 5 tests in 0.047s 226: 226: OK 225: [09:08:56] the useCache argument is deprecated and ignored 208/230 Test #208: pyMolStandardize ....................... Passed 7.70 sec 209/230 Test #222: pyMatCalc .............................. Passed 1.23 sec test 228 Start 228: pyFeatures 228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/Wrap/testFeatures.py" 228: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap 228: Test timeout computed to be: 1500 test 229 Start 229: pythonProjectTests 229: Test command: /usr/bin/python3 "-m" "pytest" 229: Working Directory: /build/reproducible-path/rdkit-202409.2/Projects 229: Test timeout computed to be: 1500 227: ----------------------------------------- 227: Test1 227: Done 210/230 Test #227: testChemicalFeatures ................... Passed 0.03 sec test 230 Start 230: pythonSourceTests 230: Test command: /usr/bin/python3 "-m" "pytest" 230: Working Directory: /build/reproducible-path/rdkit-202409.2/rdkit 230: Test timeout computed to be: 1500 211/230 Test #226: pyRanker ............................... Passed 0.76 sec 225: ...[09:08:56] the useCache argument is deprecated and ignored 225: [09:08:56] the useCache argument is deprecated and ignored 225: .[09:08:56] the useCache argument is deprecated and ignored 27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 219: .. 219: ---------------------------------------------------------------------- 219: Ran 2 tests in 1.050s 219: 219: OK 228: .. 228: ---------------------------------------------------------------------- 228: Ran 2 tests in 0.048s 228: 228: OK 228: Testing ChemicalFeatures Wrapper code: 212/230 Test #219: pyMolProcessing ........................ Passed 2.02 sec 213/230 Test #228: pyFeatures ............................. Passed 0.78 sec 191: ..[09:08:57] 191: 191: **** 191: Pre-condition Violation 191: no owner 191: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 191: Failed Expression: dp_mol 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 5# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 16# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 26# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x0000000000546E76 in /usr/bin/python3 191: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 31# _PyObject_Call_Prepend in /usr/bin/python3 191: 32# 0x000000000059D6E4 in /usr/bin/python3 191: 33# _PyObject_MakeTpCall in /usr/bin/python3 191: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 35# 0x0000000000546E76 in /usr/bin/python3 191: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 37# _PyObject_Call_Prepend in /usr/bin/python3 191: 38# 0x000000000059D6E4 in /usr/bin/python3 191: 39# _PyObject_MakeTpCall in /usr/bin/python3 191: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 41# 0x0000000000546E76 in /usr/bin/python3 191: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 43# _PyObject_Call_Prepend in /usr/bin/python3 191: 44# 0x000000000059D6E4 in /usr/bin/python3 191: 45# _PyObject_MakeTpCall in /usr/bin/python3 191: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 47# _PyObject_Call_Prepend in /usr/bin/python3 191: 48# 0x000000000059810D in /usr/bin/python3 191: 49# 0x0000000000593E22 in /usr/bin/python3 191: 50# _PyObject_MakeTpCall in /usr/bin/python3 191: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 52# PyEval_EvalCode in /usr/bin/python3 191: 53# 0x00000000005FFE7F in /usr/bin/python3 191: 54# 0x00000000006A59F2 in /usr/bin/python3 191: 55# _PyRun_SimpleFileObject in /usr/bin/python3 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 191: 59# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: [09:08:57] 191: 191: **** 191: Pre-condition Violation 191: no owner 191: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 191: Failed Expression: dp_mol 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 3# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 32# _PyObject_Call_Prepend in /usr/bin/python3 191: 33# 0x000000000059D6E4 in /usr/bin/python3 191: 34# _PyObject_MakeTpCall in /usr/bin/python3 191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 36# 0x0000000000546E76 in /usr/bin/python3 191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 38# _PyObject_Call_Prepend in /usr/bin/python3 191: 39# 0x000000000059D6E4 in /usr/bin/python3 191: 40# _PyObject_MakeTpCall in /usr/bin/python3 191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 42# 0x0000000000546E76 in /usr/bin/python3 191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 44# _PyObject_Call_Prepend in /usr/bin/python3 191: 45# 0x000000000059D6E4 in /usr/bin/python3 191: 46# _PyObject_MakeTpCall in /usr/bin/python3 191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 48# _PyObject_Call_Prepend in /usr/bin/python3 191: 49# 0x000000000059810D in /usr/bin/python3 191: 50# 0x0000000000593E22 in /usr/bin/python3 191: 51# _PyObject_MakeTpCall in /usr/bin/python3 191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 53# PyEval_EvalCode in /usr/bin/python3 191: 54# 0x00000000005FFE7F in /usr/bin/python3 191: 55# 0x00000000006A59F2 in /usr/bin/python3 191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: [09:08:57] 191: 191: **** 191: Pre-condition Violation 191: no owner 191: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 191: Failed Expression: dp_mol 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 3# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 32# _PyObject_Call_Prepend in /usr/bin/python3 191: 33# 0x000000000059D6E4 in /usr/bin/python3 191: 34# _PyObject_MakeTpCall in /usr/bin/python3 191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 36# 0x0000000000546E76 in /usr/bin/python3 191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 38# _PyObject_Call_Prepend in /usr/bin/python3 191: 39# 0x000000000059D6E4 in /usr/bin/python3 191: 40# _PyObject_MakeTpCall in /usr/bin/python3 191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 42# 0x0000000000546E76 in /usr/bin/python3 191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 44# _PyObject_Call_Prepend in /usr/bin/python3 191: 45# 0x000000000059D6E4 in /usr/bin/python3 191: 46# _PyObject_MakeTpCall in /usr/bin/python3 191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 48# _PyObject_Call_Prepend in /usr/bin/python3 191: 49# 0x000000000059810D in /usr/bin/python3 191: 50# 0x0000000000593E22 in /usr/bin/python3 191: 51# _PyObject_MakeTpCall in /usr/bin/python3 191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 53# PyEval_EvalCode in /usr/bin/python3 191: 54# 0x00000000005FFE7F in /usr/bin/python3 191: 55# 0x00000000006A59F2 in /usr/bin/python3 191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: [09:08:57] 191: 191: **** 191: Pre-condition Violation 191: no owner 191: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 191: Failed Expression: dp_mol 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 3# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 32# _PyObject_Call_Prepend in /usr/bin/python3 191: 33# 0x000000000059D6E4 in /usr/bin/python3 191: 34# _PyObject_MakeTpCall in /usr/bin/python3 191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 36# 0x0000000000546E76 in /usr/bin/python3 191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 38# _PyObject_Call_Prepend in /usr/bin/python3 191: 39# 0x000000000059D6E4 in /usr/bin/python3 191: 40# _PyObject_MakeTpCall in /usr/bin/python3 191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 42# 0x0000000000546E76 in /usr/bin/python3 191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 44# _PyObject_Call_Prepend in /usr/bin/python3 191: 45# 0x000000000059D6E4 in /usr/bin/python3 191: 46# _PyObject_MakeTpCall in /usr/bin/python3 191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 48# _PyObject_Call_Prepend in /usr/bin/python3 191: 49# 0x000000000059810D in /usr/bin/python3 191: 50# 0x0000000000593E22 in /usr/bin/python3 191: 51# _PyObject_MakeTpCall in /usr/bin/python3 191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 53# PyEval_EvalCode in /usr/bin/python3 191: 54# 0x00000000005FFE7F in /usr/bin/python3 191: 55# 0x00000000006A59F2 in /usr/bin/python3 191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: [09:08:57] 191: 191: **** 191: Pre-condition Violation 191: no owner 191: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h 191: Failed Expression: dp_mol 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 3# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 32# _PyObject_Call_Prepend in /usr/bin/python3 191: 33# 0x000000000059D6E4 in /usr/bin/python3 191: 34# _PyObject_MakeTpCall in /usr/bin/python3 191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 36# 0x0000000000546E76 in /usr/bin/python3 191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 38# _PyObject_Call_Prepend in /usr/bin/python3 191: 39# 0x000000000059D6E4 in /usr/bin/python3 191: 40# _PyObject_MakeTpCall in /usr/bin/python3 191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 42# 0x0000000000546E76 in /usr/bin/python3 191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 44# _PyObject_Call_Prepend in /usr/bin/python3 191: 45# 0x000000000059D6E4 in /usr/bin/python3 191: 46# _PyObject_MakeTpCall in /usr/bin/python3 191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 48# _PyObject_Call_Prepend in /usr/bin/python3 191: 49# 0x000000000059810D in /usr/bin/python3 191: 50# 0x0000000000593E22 in /usr/bin/python3 191: 51# _PyObject_MakeTpCall in /usr/bin/python3 191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 53# PyEval_EvalCode in /usr/bin/python3 191: 54# 0x00000000005FFE7F in /usr/bin/python3 191: 55# 0x00000000006A59F2 in /usr/bin/python3 191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: .....[09:08:57] 191: 191: **** 191: Range Error 191: atomIdx1 191: Violation occurred on line 496 in file ./Code/GraphMol/RWMol.cpp 191: Failed Expression: 0 < 0 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 5# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 16# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 26# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x0000000000546E76 in /usr/bin/python3 191: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 31# _PyObject_Call_Prepend in /usr/bin/python3 191: 32# 0x000000000059D6E4 in /usr/bin/python3 191: 33# _PyObject_MakeTpCall in /usr/bin/python3 191: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 35# 0x0000000000546E76 in /usr/bin/python3 191: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 37# _PyObject_Call_Prepend in /usr/bin/python3 191: 38# 0x000000000059D6E4 in /usr/bin/python3 191: 39# _PyObject_MakeTpCall in /usr/bin/python3 191: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 41# 0x0000000000546E76 in /usr/bin/python3 191: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 43# _PyObject_Call_Prepend in /usr/bin/python3 191: 44# 0x000000000059D6E4 in /usr/bin/python3 191: 45# _PyObject_MakeTpCall in /usr/bin/python3 191: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 47# _PyObject_Call_Prepend in /usr/bin/python3 191: 48# 0x000000000059810D in /usr/bin/python3 191: 49# 0x0000000000593E22 in /usr/bin/python3 191: 50# _PyObject_MakeTpCall in /usr/bin/python3 191: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 52# PyEval_EvalCode in /usr/bin/python3 191: 53# 0x00000000005FFE7F in /usr/bin/python3 191: 54# 0x00000000006A59F2 in /usr/bin/python3 191: 55# _PyRun_SimpleFileObject in /usr/bin/python3 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 191: 59# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: ......[09:08:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 191: [09:08:57] ERROR: Smiles parse error on line 0 191: [09:08:57] ERROR: Cannot create molecule from : 'c1ccccc' 191: [09:08:57] SMILES Parse Error: extra open parentheses for input: 'C(C' 191: [09:08:57] ERROR: Smiles parse error on line 3 191: [09:08:57] ERROR: Cannot create molecule from : 'C(C' 191: [09:08:57] Explicit valence for atom # 1 C, 5, is greater than permitted 191: [09:08:57] ERROR: Could not sanitize molecule on line 6 191: [09:08:57] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 191: [09:08:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 191: [09:08:57] ERROR: Smiles parse error on line 0 191: [09:08:57] ERROR: Cannot create molecule from : 'c1ccccc' 191: [09:08:57] SMILES Parse Error: extra open parentheses for input: 'C(C' 191: [09:08:57] ERROR: Smiles parse error on line 3 191: [09:08:57] ERROR: Cannot create molecule from : 'C(C' 191: [09:08:57] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' 191: [09:08:57] ERROR: Smiles parse error on line 6 191: [09:08:57] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' 191: [09:08:57] Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:57] ERROR: Could not sanitize molecule ending on line 21 191: [09:08:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:57] ERROR: EOF hit while reading atoms 191: [09:08:57] ERROR: moving to the beginning of the next molecule 191: [09:08:57] Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:57] ERROR: Could not sanitize molecule ending on line 21 191: [09:08:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:57] ERROR: EOF hit while reading atoms 191: [09:08:57] ERROR: moving to the beginning of the next molecule 27: All 191 tests passed 27: done 27: ------------------------------------- 27: Unit tests for all MMFF constraint terms. 191: ....[09:08:57] 191: 191: **** 191: Pre-condition Violation 191: RingInfo not initialized 191: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp 191: Failed Expression: df_init 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 5# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 16# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 26# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x0000000000546E76 in /usr/bin/python3 191: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 31# _PyObject_Call_Prepend in /usr/bin/python3 191: 32# 0x000000000059D6E4 in /usr/bin/python3 191: 33# _PyObject_MakeTpCall in /usr/bin/python3 191: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 35# 0x0000000000546E76 in /usr/bin/python3 191: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 37# _PyObject_Call_Prepend in /usr/bin/python3 191: 38# 0x000000000059D6E4 in /usr/bin/python3 191: 39# _PyObject_MakeTpCall in /usr/bin/python3 191: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 41# 0x0000000000546E76 in /usr/bin/python3 191: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 43# _PyObject_Call_Prepend in /usr/bin/python3 191: 44# 0x000000000059D6E4 in /usr/bin/python3 191: 45# _PyObject_MakeTpCall in /usr/bin/python3 191: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 47# _PyObject_Call_Prepend in /usr/bin/python3 191: 48# 0x000000000059810D in /usr/bin/python3 191: 49# 0x0000000000593E22 in /usr/bin/python3 191: 50# _PyObject_MakeTpCall in /usr/bin/python3 191: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 52# PyEval_EvalCode in /usr/bin/python3 191: 53# 0x00000000005FFE7F in /usr/bin/python3 191: 54# 0x00000000006A59F2 in /usr/bin/python3 191: 55# _PyRun_SimpleFileObject in /usr/bin/python3 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 191: 59# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: ............[09:08:57] 191: 191: **** 191: Range Error 191: idx 191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp 191: Failed Expression: 3 < 1 191: ---------- 191: Stacktrace: 191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 5# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so 191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so 191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 16# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 17# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 18# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 19# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 20# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 26# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x0000000000546E76 in /usr/bin/python3 191: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 31# _PyObject_Call_Prepend in /usr/bin/python3 191: 32# 0x000000000059D6E4 in /usr/bin/python3 191: 33# _PyObject_MakeTpCall in /usr/bin/python3 191: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 35# 0x0000000000546E76 in /usr/bin/python3 191: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 37# _PyObject_Call_Prepend in /usr/bin/python3 191: 38# 0x000000000059D6E4 in /usr/bin/python3 191: 39# _PyObject_MakeTpCall in /usr/bin/python3 191: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 41# 0x0000000000546E76 in /usr/bin/python3 191: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 43# _PyObject_Call_Prepend in /usr/bin/python3 191: 44# 0x000000000059D6E4 in /usr/bin/python3 191: 45# _PyObject_MakeTpCall in /usr/bin/python3 191: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 47# _PyObject_Call_Prepend in /usr/bin/python3 191: 48# 0x000000000059810D in /usr/bin/python3 191: 49# 0x0000000000593E22 in /usr/bin/python3 191: 50# _PyObject_MakeTpCall in /usr/bin/python3 191: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 52# PyEval_EvalCode in /usr/bin/python3 191: 53# 0x00000000005FFE7F in /usr/bin/python3 191: 54# 0x00000000006A59F2 in /usr/bin/python3 191: 55# _PyRun_SimpleFileObject in /usr/bin/python3 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 191: 59# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: 191: ...[09:08:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 27: 10.0003 27: done 27: ------------------------------------- 27: Unit test for MMFF TorsionConstraint close to 0 degrees. 27: done 27: ------------------------------------- 27: Unit tests for copying MMFF ForceFields. 27: done 27: ------------------------------------- 27: Unit test for MMFF butane scan. 191: ............................[09:08:57] SMILES Parse Error: unclosed ring for input: 'C1CC' 191: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| 191: 323 191: ..[09:08:57] WARNING: not removing hydrogen atom without neighbors 191: [09:08:57] WARNING: not removing hydrogen atom with dummy atom neighbors 191: [09:08:57] WARNING: not removing hydrogen atom with wedged bond 191: [09:08:57] WARNING: not removing hydrogen atom without neighbors 191: [09:08:57] WARNING: not removing hydrogen atom with dummy atom neighbors 27: done 214/230 Test #27: testMMFFForceField ..................... Passed 45.01 sec 230: ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. 230: __init__.py:6: in 230: from . import rdBase 230: E ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/build/reproducible-path/rdkit-202409.2/rdkit/__init__.py) 215/230 Test #230: pythonSourceTests ......................***Failed 1.83 sec ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. __init__.py:6: in from . import rdBase E ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/build/reproducible-path/rdkit-202409.2/rdkit/__init__.py) 191: ......[09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 191: .[09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted 191: [09:08:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 191: [09:08:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 191: [09:08:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 191: ..........[09:08:58] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 191: [09:08:58] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 191: .[09:08:58] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 191: ..[09:08:58] SMILES Parse Error: syntax error while parsing: error 191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' 191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' 191: [09:08:58] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' 191: [09:08:58] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' 191: .........................[09:08:58] SMILES Parse Error: syntax error while parsing: garbage_0 191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' 191: [09:08:58] SMILES Parse Error: syntax error while parsing: garbage_2 191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' 191: [09:08:58] SMILES Parse Error: syntax error while parsing: garbage_4 191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 191: ........... 191: ---------------------------------------------------------------------- 191: Ran 277 tests in 14.892s 191: 191: OK 191: supplier: 191: supplier: 191: supplier: 216/230 Test #191: pyGraphMolWrap ......................... Passed 16.14 sec 225: ....... 225: ---------------------------------------------------------------------- 225: Ran 11 tests in 2.310s 225: 225: OK 217/230 Test #225: pySimDivPickers ........................ Passed 3.07 sec 218/230 Test #195: pyTestThreads .......................... Passed 14.23 sec 229: ============================= test session starts ============================== 229: platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 229: rootdir: /build/reproducible-path/rdkit-202409.2/Projects 229: configfile: pytest.ini 229: plugins: typeguard-4.4.1 229: collected 12 items 229: 148: --------------------------------- 148: test O3A multithreading bug 148: 148: --------------------------------- 148: testCrippenO3A multithreading 148: 148: generating reference data 181: ......[09:09:00] 181: 181: **** 181: Pre-condition Violation 181: RingInfo not initialized 181: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp 181: Failed Expression: df_init 181: ---------- 181: Stacktrace: 181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 181: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 181: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 181: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 181: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 12# 0x00007EFC8E8552B5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 14# 0x00007EFC9128B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 181: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 181: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 181: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 20# 0x00007EFC8E7AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 21# 0x00007EFC8E7AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 22# 0x00007EFC8E7AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 23# 0x00007EFC8E7AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 24# 0x00007EFC8E7AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 181: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 181: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 181: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 181: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 30# 0x00007EFC912883C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 31# _PyObject_MakeTpCall in /usr/bin/python3 181: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 33# 0x0000000000546E76 in /usr/bin/python3 181: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 35# _PyObject_Call_Prepend in /usr/bin/python3 181: 36# 0x000000000059D6E4 in /usr/bin/python3 181: 37# _PyObject_MakeTpCall in /usr/bin/python3 181: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 39# 0x0000000000546E76 in /usr/bin/python3 181: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 41# _PyObject_Call_Prepend in /usr/bin/python3 181: 42# 0x000000000059D6E4 in /usr/bin/python3 181: 43# _PyObject_MakeTpCall in /usr/bin/python3 181: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 45# 0x0000000000546E76 in /usr/bin/python3 181: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 47# _PyObject_Call_Prepend in /usr/bin/python3 181: 48# 0x000000000059D6E4 in /usr/bin/python3 181: 49# _PyObject_MakeTpCall in /usr/bin/python3 181: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 51# _PyObject_Call_Prepend in /usr/bin/python3 181: 52# 0x000000000059810D in /usr/bin/python3 181: 53# 0x0000000000593E22 in /usr/bin/python3 181: 54# _PyObject_MakeTpCall in /usr/bin/python3 181: 55# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 56# PyEval_EvalCode in /usr/bin/python3 181: 57# 0x00000000005FFE7F in /usr/bin/python3 181: 58# 0x00000000006A59F2 in /usr/bin/python3 181: 59# _PyRun_SimpleFileObject in /usr/bin/python3 181: 60# _PyRun_AnyFileObject in /usr/bin/python3 181: 61# Py_RunMain in /usr/bin/python3 181: 62# Py_BytesMain in /usr/bin/python3 181: 63# 0x00007EFC91A41D68 in /lib/x86_64-linux-gnu/libc.so.6 181: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 181: 65# _start in /usr/bin/python3 181: ---------- 181: **** 181: 181: [09:09:00] 181: 181: **** 181: Pre-condition Violation 181: RingInfo not initialized 181: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp 181: Failed Expression: df_init 181: ---------- 181: Stacktrace: 181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 181: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 181: 3# 0x00007EFC8E2E5020 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 181: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 181: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 181: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 13# 0x00007EFC8E8552B5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 15# 0x00007EFC9128B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 181: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 181: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 181: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 21# 0x00007EFC8E7AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 22# 0x00007EFC8E7AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 23# 0x00007EFC8E7AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 24# 0x00007EFC8E7AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 25# 0x00007EFC8E7AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 181: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 181: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 181: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 181: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/rdBase.so 181: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 31# 0x00007EFC912883C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 181: 32# _PyObject_MakeTpCall in /usr/bin/python3 181: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 34# 0x0000000000546E76 in /usr/bin/python3 181: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 36# _PyObject_Call_Prepend in /usr/bin/python3 181: 37# 0x000000000059D6E4 in /usr/bin/python3 181: 38# _PyObject_MakeTpCall in /usr/bin/python3 181: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 40# 0x0000000000546E76 in /usr/bin/python3 181: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 42# _PyObject_Call_Prepend in /usr/bin/python3 181: 43# 0x000000000059D6E4 in /usr/bin/python3 181: 44# _PyObject_MakeTpCall in /usr/bin/python3 181: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 46# 0x0000000000546E76 in /usr/bin/python3 181: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 48# _PyObject_Call_Prepend in /usr/bin/python3 181: 49# 0x000000000059D6E4 in /usr/bin/python3 181: 50# _PyObject_MakeTpCall in /usr/bin/python3 181: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 52# _PyObject_Call_Prepend in /usr/bin/python3 181: 53# 0x000000000059810D in /usr/bin/python3 181: 54# 0x0000000000593E22 in /usr/bin/python3 181: 55# _PyObject_MakeTpCall in /usr/bin/python3 181: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 181: 57# PyEval_EvalCode in /usr/bin/python3 181: 58# 0x00000000005FFE7F in /usr/bin/python3 181: 59# 0x00000000006A59F2 in /usr/bin/python3 181: 60# _PyRun_SimpleFileObject in /usr/bin/python3 181: 61# _PyRun_AnyFileObject in /usr/bin/python3 181: 62# Py_RunMain in /usr/bin/python3 181: 63# Py_BytesMain in /usr/bin/python3 181: 64# 0x00007EFC91A41D68 in /lib/x86_64-linux-gnu/libc.so.6 181: 65# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 181: 66# _start in /usr/bin/python3 181: ---------- 181: **** 181: 148: processing 148: launch :0 148: launch :1 148: launch :2 148: launch :3 218: Randomness seeded to: 4090292774 218: =============================================================================== 218: All tests passed (203 assertions in 1 test case) 218: 219/230 Test #218: testMolProcessing ...................... Passed 5.69 sec 146: .........[09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: .[09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: .[09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() 181: ............. 181: ---------------------------------------------------------------------- 181: Ran 19 tests in 25.483s 181: 181: OK 181: Testing atom rings 181: testing bond rings 181: searching atom rings 181: searching bond rings 181: done 220/230 Test #181: pySubstructLibrary ..................... Passed 26.04 sec 146: ... 146: ---------------------------------------------------------------------- 146: Ran 22 tests in 47.238s 146: 146: OK 221/230 Test #146: pyDistGeomHelpers ...................... Passed 48.25 sec 206: [09:09:10] Explicit valence for atom # 0 Br, 1, is greater than permitted 206: =============================================================================== 206: All tests passed (38339 assertions in 50 test cases) 206: 222/230 Test #206: molStandardizeCatchTest ................ Passed 22.75 sec 148: --------------------------------- 148: test getO3AForProbeConfs 148: 148: *********************************************************** 223/230 Test #148: testO3AAlign ........................... Passed 53.25 sec 145: [09:09:27] UFFTYPER: Unrecognized atom type: S_6+6 (0) 145: [09:09:27] UFFTYPER: Warning: hybridization set to SP3 for atom 0 145: [09:09:27] UFFTYPER: Unrecognized charge state for atom: 0 31: [09:09:38] Finished 31: [09:09:38] ------------------------------------- 31: [09:09:38] Test github1843: RWMol.clear() should not destroy ring pointer. 31: [09:09:38] Finished 31: [09:09:38] ------------------------------------- 31: [09:09:38] Test Github 6370: non-physical radical counts being preserved 31: [09:09:38] Finished 224/230 Test #31: graphmolTest1 .......................... Passed 85.55 sec 144: [09:09:46] done 144: [09:09:46] --------------------------------- 144: [09:09:46] test github issue 256: handling of zero-atom molecules 144: 144: [09:09:46] --------------------------------- 144: [09:09:46] test embedder callback function 144: [09:09:46] --------------------------------- 144: [09:09:46] test multi-threaded multi-conf embedding 144: 144: [09:09:52] --------------------------------- 144: [09:09:52] test github issue 563: Incorrect ring stereochemistry after embedding 144: 144: CNC[C@H]1CC[C@H](C[NH3+])CC1 169: =============================================================================== 169: All tests passed (93 assertions in 5 test cases) 169: 225/230 Test #169: testRascalCluster ...................... Passed 84.56 sec 144: [09:09:55] --------------------------------- 144: [09:09:55] test github issue 568: Incorrect stereochemistry after embedding 144: 144: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 168: =============================================================================== 168: All tests passed (2923 assertions in 27 test cases) 168: 226/230 Test #168: testRascalMCES ......................... Passed 86.66 sec 144: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 144: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 144: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 144: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 144: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 144: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 144: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 144: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 144: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 144: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 144: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 144: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 144: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 144: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 144: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 144: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 144: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 145: =============================================================================== 145: All tests passed (12735 assertions in 18 test cases) 145: 227/230 Test #145: distGeomHelpersCatch ................... Passed 113.94 sec 5: [09:10:15] Finished: testMultipleTimes() 5: [09:10:15] 5: ----------------------------------------- 228/230 Test #5: testConcurrentQueue .................... Passed 122.39 sec 144: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 144: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 144: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 144: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 144: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 144: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 144: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 144: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 144: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 144: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] 229: DbCLI/UnitTestDbCLI.py ............ [100%] 229: 229: =============================== warnings summary =============================== 229: ../obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 229: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) 229: decBase = declarative_base() 229: 229: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 229: =================== 12 passed, 1 warning in 92.03s (0:01:32) =================== 229/230 Test #229: pythonProjectTests ..................... Passed 94.25 sec 144: [09:10:42] Molecule does not have explicit Hs. Consider calling AddHs() 144: [09:10:30] --------------------------------- 144: [09:10:30] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system 144: [09:10:30] --------------------------------- 144: [09:10:30] More ChEMBL molecules failing bounds smoothing. 144: [09:10:30] --------------------------------- 144: [09:10:30] ugly conformations can be generated for highly constrained ring systems. 144: [09:10:30] --------------------------------- 144: [09:10:30] test embed parameters structure. 144: [09:10:30] --------------------------------- 144: [09:10:30] test github 1227: Hs being used in RMSD filtering. 144: [09:10:30] --------------------------------- 144: [09:10:30] Failure to embed larger aromatic rings. 144: [09:10:34] --------------------------------- 144: [09:10:34] Deterministic with large random seeds 144: [09:10:39] --------------------------------- 144: [09:10:39] Github #1990: seg fault after RemoveHs 144: [09:10:39] --------------------------------- 144: [09:10:39] Github #2246: Use coordMap when starting embedding from random coords 144: [09:10:41] --------------------------------- 144: [09:10:41] Providing a distance bounds matrix. 144: [09:10:41] --------------------------------- 144: [09:10:41] Disabling fragmentation. 144: [09:10:41] --------------------------------- 144: [09:10:41] Using symmetry in conformation pruning. 144: [09:10:42] --------------------------------- 144: [09:10:42] Force trans amides. 144: [09:10:42] --------------------------------- 144: [09:10:42] test missing Hs warning. 144: [09:10:42] --------------------------------- 144: [09:10:42] basic H bond support. 144: [09:10:42] ******************************************************* 230/230 Test #144: testDistGeomHelpers .................... Passed 141.30 sec 99% tests passed, 1 tests failed out of 230 Total Test time (real) = 149.33 sec The following tests FAILED: 230 - pythonSourceTests (Failed) Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 returned exit code 2 make[1]: [debian/rules:149: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_installdirs -O--buildsystem=cmake debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_auto_install cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/rdkit-202409.2/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.2 -B/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__pycache__ -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__pycache__/__init__.cpython-312.pyc -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemutils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw_qax.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/retest.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/listutils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/cactvs.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/spiral.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/fileutils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt4.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/Fontmapping.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/pidPyart.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/pidSVG.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/colors.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/stringformat.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pagesizes.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgen.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgeom.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfdoc.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfutils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pidtest.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pstests.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil -- Installing: 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Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Murtagh.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterUtils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Butina.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterVis.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Standardize.py -- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/Scoring.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/Risk.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitRank.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitClusterer.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/entropy.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/files.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/Descriptors.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/Parser.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Transforms.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Quantize.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/FindQuantBounds.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/SplitData.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/MLData.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/DataUtils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Stats.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/conftest.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/rddata.sql -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Salts.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Crippen.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/RDData.sqlt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/test_data -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/wiki -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png -- Installing: 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Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb -- Installing: 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Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDInchiLib.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/inchi.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdinchi.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/CoordGen.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdCoordGen.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitga.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitga.so.1 -- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/FileParseException.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/Invariant.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDAny.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDValue.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDValue-doublemagic.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDValue-taggedunion.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDLog.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDProps.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDThreads.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/StreamOps.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/types.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/utils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/versions.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDConfig.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/LocaleSwitcher.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/Ranking.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hanoiSort.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/RDExportMacros.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/export.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/test.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/ConcurrentQueue.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDBoost.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDBoost.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDBoost/Wrap.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDBoost/PySequenceHolder.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDBoost/list_indexing_suite.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDBoost/python.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDBoost/boost_numpy.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDBoost/python_streambuf.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDBoost/pyint_api.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/rdBase.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDStreams.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDStreams.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDStreams.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDStreams/streams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDataStructs.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDataStructs.so.1 -- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DataStructs/DiscreteValueVect.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DataStructs/ExplicitBitVect.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DataStructs/SparseBitVect.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DataStructs/SparseIntVect.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DataStructs/FPBReader.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DataStructs/MultiFPBReader.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/cDataStructs.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDGeometryLib.so.1.2024.09.2 -- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Numerics/Vector.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Numerics/Conrec.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitForceField.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitForceField.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitForceField.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/Contrib.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/ForceField.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/AngleConstraints.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraints.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h -- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField/rdForceField.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDistGeometry.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDistGeometry.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContribs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContribs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContrib.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContribs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry/DistGeom.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitCatalogs.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitCatalogs.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGraphMol.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGraphMol.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Atom.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Atropisomers.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Bond.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Canon.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/details.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Rings.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSmilesParse.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/primes.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/CanonicalizeStereoGroups.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDepictor.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDepictor.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDepictor.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdDepictor.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMarvinParser.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMarvinParser.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMarvinParser.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MarvinParse/MarvinParser.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFileParsers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFileParsers.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/CDXMLParser.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileWriters.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.v1API.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubstructMatch.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGenericGroups.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGenericGroups.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGenericGroups.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/GenericGroups/GenericGroups.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemReactions.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemReactions.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdChemReactions.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemTransforms.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubgraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubgraphs.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFilterCatalog.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdfiltercatalog.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFragCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFragCatalog.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdfragcatalog.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDescriptors.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDescriptors.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolSurf.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MQN.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Property.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AtomFeat.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/OxidationNumbers.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/DCLV.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/EEM.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PBF.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PMI.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RDF.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MORSE.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/GETAWAY.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/WHIM.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/CoulombMat.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolDescriptors.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFingerprints.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFingerprints.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/Fingerprints.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MACCS.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MHFP.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdFingerprintGenerator.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMHFPFingerprint.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitPartialCharges.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolTransforms.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/FFConvenience.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/UFF.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdDistGeom.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolAlign.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitO3AAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitO3AAlign.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolAlign.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/rdMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFMCS.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFMCS.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitFMCS.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FMCS/FMCS.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdFMCS.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolHash.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolHash.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolHash.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolHash.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMMPA.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMMPA.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMMPA.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMMPA.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRascalMCES.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRascalMCES.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalMCES.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalOptions.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalClusterOptions.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalResult.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/CIPLabeler/CIPLabeler.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/CIPLabeler/TooManyNodesException.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDeprotect.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitDeprotect.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdDeprotect.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitTrajectory.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitTrajectory.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolInterchange.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSLNParse.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSLNParse.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSLNParse.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNAttribs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParse.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParseOps.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdSLNParse.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdchem.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdmolops.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdqueries.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdmolfiles.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdtrajectory.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolStandardize.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Pipeline.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/LinkNode.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitAbbreviations.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/GeneralizedSubstruct/XQMol.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdGeneralizedSubstruct.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolProcessing.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolProcessing.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitMolProcessing.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/GraphMol/MolProcessing/MolProcessing.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolProcessing.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/AndQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/LessQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/OrQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/Query.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/QueryObjects.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/RangeQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/SetQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Query/XOrQuery.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/Features/Feature.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKithc.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKithc.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKithc.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/cQuantize.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdChemicalFeatures.so ===================================================================== PostgreSQL cartridge installation succeeded. ===================================================================== Restart the PostgreSQL service before using the PostgreSQL RDKit cartridge. ===================================================================== -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDPaths.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' mkdir -p /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3 mv /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3/dist-packages rm -f -rf /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12 ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf dh_install -ppython3-rdkit /usr/lib/python3 rm -f -rf /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ rm -f -rf /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/__pycache__ dh_numpy3 dh_install for v in $(pg_buildext supported-versions); do \ mkdir -p debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/ debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/build-$v/librdkit.so debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/rdkit.so; \ cp Code/PgSQL/rdkit/build-$v/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/build-$v/update_sql/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ cp Code/PgSQL/rdkit/rdkit.control debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ done mkdir -p /build/reproducible-path/rdkit-202409.2/debian/rdkit-doc/usr/share/doc/rdkit/ # cp /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202409.2/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html /build/reproducible-path/rdkit-202409.2/debian/rdkit-doc/usr/share/doc/rdkit/ ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202409.2/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202409.2/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202409.2/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' dh_installdocs -O--buildsystem=cmake debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_python3 -ppython3-rdkit I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdCoordGen.so to rdCoordGen.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdDepictor.so to rdDepictor.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdDeprotect.so to rdDeprotect.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdDistGeom.so to rdDistGeom.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdFMCS.so to rdFMCS.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeneralizedSubstruct.so to rdGeneralizedSubstruct.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMMPA.so to rdMMPA.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolAlign.so to rdMolAlign.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolCatalog.so to rdMolCatalog.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolHash.so to rdMolHash.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolInterchange.so to rdMolInterchange.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolProcessing.so to rdMolProcessing.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolTransforms.so to rdMolTransforms.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdPartialCharges.so to rdPartialCharges.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdRascalMCES.so to rdRascalMCES.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdSLNParse.so to rdSLNParse.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdchem.so to rdchem.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdfragcatalog.so to rdfragcatalog.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdinchi.so to rdinchi.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdmolfiles.so to rdmolfiles.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdmolops.so to rdmolops.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdqueries.so to rdqueries.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdtrajectory.so to rdtrajectory.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-312-x86_64-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_missing --list-missing dh_missing: warning: usr/lib/postgresql/17/lib/rdkit.so exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv exists in 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usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/solubility.test.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/solubility.train.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/test_multi_colours.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/exts/extapi.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png exists in debian/tmp but is not installed to anywhere 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usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: 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usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/terminology_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/CIPLabeling.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/CodingStandards.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/EnhancedStereo.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/SGroups.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.lrg.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo_plain.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/compounds.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/RD.css exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/FeatFinderCLI.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/PythonFormat.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/create_deb_packages.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/test.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/license.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--3.8--4.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0--4.0.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0.1--4.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1--4.1.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1.1--4.2.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.2--4.3.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.3.0--4.4.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.4.0--4.5.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.5.0--4.6.0.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.0--4.6.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.1.sql exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/postgresql/17/extension/rdkit.control exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: librdkit-dev (62), librdkit1t64 (120), postgresql-17-rdkit (0), python3-rdkit (1), rdkit-data (3), rdkit-doc (0) * dh_installdocs: librdkit-dev (0), librdkit1t64 (0), postgresql-17-rdkit (0), python3-rdkit (0), rdkit-data (0), rdkit-doc (0) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol errcode: it's probably a plugin dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} 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 rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.2-2_amd64.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.2-2_amd64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.2-2_all.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.2-2_all.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.2-2_amd64.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.2-2_amd64.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.2-2_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.2-2_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.2-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202409.2-2_amd64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202409.2-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/3972870 and its subdirectories I: Current time: Tue Dec 17 09:19:42 -12 2024 I: pbuilder-time-stamp: 1734470382 Tue Dec 17 21:19:45 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Tue Dec 17 21:19:45 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Tue Dec 17 21:36:26 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Tue Dec 17 21:36:27 UTC 2024 I: rdkit_202409.2-2_amd64.changes: Format: 1.8 Date: Wed, 27 Nov 2024 20:11:03 +0100 Source: rdkit Binary: librdkit-dev librdkit1t64 librdkit1t64-dbgsym postgresql-17-rdkit postgresql-17-rdkit-dbgsym python3-rdkit python3-rdkit-dbgsym rdkit-data rdkit-doc Architecture: amd64 all Version: 202409.2-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Michael Banck Description: librdkit-dev - Collection of cheminformatics and machine-learning software (deve librdkit1t64 - Collection of cheminformatics and machine-learning software (shar postgresql-17-rdkit - Cheminformatics and machine-learning software (PostgreSQL Cartrid python3-rdkit - Collection of cheminformatics and machine-learning software rdkit-data - Collection of cheminformatics and machine-learning software (data rdkit-doc - Collection of cheminformatics and machine-learning software (docu Closes: 1088354 Changes: rdkit (202409.2-2) unstable; urgency=medium . * debian/rules (DH_AUTO_CONFIGURE_OPTS): Added -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF (Closes: #1088354). Checksums-Sha1: ccb0d99d1a4d70cb769c772c4ef017e22aba7b74 456984 librdkit-dev_202409.2-2_amd64.deb 23034b2f00d90b2cceff03bb82dfed9e9ddcecb6 114522452 librdkit1t64-dbgsym_202409.2-2_amd64.deb 9e9b6537d8e47811fbf2618da70c69c28e087660 5341488 librdkit1t64_202409.2-2_amd64.deb 52499473088fb5c5fd928436eb57c6420102faee 1163860 postgresql-17-rdkit-dbgsym_202409.2-2_amd64.deb 72b79de3d06ac7b3e548117d77f6a639b4e63bea 244212 postgresql-17-rdkit_202409.2-2_amd64.deb c883fad7c524a0a8db2e2e6f963cb5f070885fbd 61221412 python3-rdkit-dbgsym_202409.2-2_amd64.deb a8295665b68d7c809f14532f75ec0cbc36e79793 4491516 python3-rdkit_202409.2-2_amd64.deb 8be2b0ae4c2f1ac607dde70622e1306c6b175d68 13158208 rdkit-data_202409.2-2_all.deb 5f815f274e69b8403a7af6e1599e17ffde5d086f 6528760 rdkit-doc_202409.2-2_all.deb bc1c7fa36be55bc1129c1eceda0a301c81ee6853 18556 rdkit_202409.2-2_amd64.buildinfo Checksums-Sha256: 8b92fefbc566b745ede577e6731583450744ec64e188b0a3b5a6924a719a999d 456984 librdkit-dev_202409.2-2_amd64.deb c8b9f7b5a7f7ce05a7c6c404a3922c6d389f10ea83de4db5a94f496714893210 114522452 librdkit1t64-dbgsym_202409.2-2_amd64.deb c3d066383d37c5a21742007b729637d0c6d2378f2cf02218fa4f17c3523d6ca0 5341488 librdkit1t64_202409.2-2_amd64.deb d20fe4ac70f113417824ef5fdd486e581352d43310be58740fca7c7a2cabdfa6 1163860 postgresql-17-rdkit-dbgsym_202409.2-2_amd64.deb c1300cc3f9903b223cc2d19966c2753a8f915ce4dbb8603637a54164148792ec 244212 postgresql-17-rdkit_202409.2-2_amd64.deb 4d17ae1868b680c76ab9741c78dabacc2266802ea81f1822b4aad58c1d4eb821 61221412 python3-rdkit-dbgsym_202409.2-2_amd64.deb f88880621e6d5e308cfa751ebd3882dd6ea7baef7fa63297c080cc76b3f66907 4491516 python3-rdkit_202409.2-2_amd64.deb 2b4bb4459eeb5f6555baea19d067113a47efe914f0209082b5b45eeb9871ff4d 13158208 rdkit-data_202409.2-2_all.deb fc0af87c56452cad6895ec6fba93aab7777514f08bfd123673e10db5acac4c94 6528760 rdkit-doc_202409.2-2_all.deb 1dbef887ab1e82f97561de52c6f6df888a050ceb313d95c69d5a247cdfcdecc4 18556 rdkit_202409.2-2_amd64.buildinfo Files: 928c3b2cb793089aabeda074b6df0980 456984 libdevel optional librdkit-dev_202409.2-2_amd64.deb 23f55097e3552cad50d96e87a1014e66 114522452 debug optional librdkit1t64-dbgsym_202409.2-2_amd64.deb 1091208879a675f6ea6ce4b06b274c05 5341488 libs optional librdkit1t64_202409.2-2_amd64.deb e8ce91f8442ca1cb518f11e84da4f315 1163860 debug optional postgresql-17-rdkit-dbgsym_202409.2-2_amd64.deb 5872bcfa3b32a519e806e3652a6e7990 244212 database optional postgresql-17-rdkit_202409.2-2_amd64.deb f9c9b88eab26f399de2c172d874f8786 61221412 debug optional python3-rdkit-dbgsym_202409.2-2_amd64.deb e7bd4ef2c3a8e073819ff9a714710395 4491516 python optional python3-rdkit_202409.2-2_amd64.deb 268062a729122037ad7230ee3bf65f9e 13158208 science optional rdkit-data_202409.2-2_all.deb 3250f2ae1c3c489bd0c631fb84a8bb43 6528760 doc optional rdkit-doc_202409.2-2_all.deb 0e624c638b44ddccbc0a364ce62cfceb 18556 science optional rdkit_202409.2-2_amd64.buildinfo Tue Dec 17 21:36:29 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_9-25943.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wWec19YJ/rdkit_202409.2-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wWec19YJ/rdkit_202409.2-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wWec19YJ/rdkit_202409.2-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wWec19YJ/b1/rdkit_202409.2-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wWec19YJ/b2/rdkit_202409.2-2_amd64.changes ## close_archive (total time: 0.001s) 0.000s 38 calls diffoscope.comparators.xz.XzContainer 0.000s 30 calls diffoscope.comparators.tar.TarContainer 0.000s 24 calls diffoscope.comparators.deb.DebContainer 0.000s 8 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 39.769s) 16.591s 1058 calls readelf 11.956s 135 calls diff 4.400s 38 calls xz 3.554s 2 calls objcopy 2.166s 220 calls objdump 0.448s 11 calls cmp 0.447s 11 calls cmp (external) 0.129s 33 calls js-beautify 0.072s 22 calls strings 0.007s 95 calls cmp (internal) ## compare_files (cumulative) (total time: 207.642s) 42.597s 1 call abc.DotChangesFile 42.292s 3 calls abc.DebFile 41.667s 6 calls abc.XzFile 38.168s 3 calls abc.DebDataTarFile 26.902s 2 calls abc.ElfFile 12.196s 10 calls diffoscope.comparators.elf.ElfCodeSection 2.790s 3 calls abc.JavaScriptFile 0.500s 37 calls diffoscope.comparators.elf.ElfSection 0.274s 3 calls abc.TarFile 0.147s 3 calls abc.Md5sumsFile 0.073s 3 calls diffoscope.comparators.elf.ElfStringSection 0.026s 2 calls abc.TextFile 0.010s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 8.889s) 4.402s 38 calls diffoscope.comparators.xz.XzContainer 3.098s 10078 calls diffoscope.comparators.deb.DebTarContainer 1.359s 44 calls diffoscope.comparators.deb.DebContainer 0.031s 40 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 1.153s) 1.153s 67 calls linediff ## has_same_content_as (total time: 0.462s) 0.317s 3 calls abc.DebDataTarFile 0.130s 9 calls abc.DebFile 0.006s 64 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.005s 6 calls abc.Md5sumsFile 0.001s 8 calls abc.TextFile 0.000s 2 calls abc.ElfFile 0.000s 6 calls abc.XzFile 0.000s 3 calls abc.TarFile 0.000s 3 calls abc.JavaScriptFile 0.000s 37 calls diffoscope.comparators.elf.ElfSection 0.000s 1 call abc.DotChangesFile 0.000s 10 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 3 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 46.173s) 46.162s 2 calls outputs 0.010s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 30 calls diffoscope.comparators.tar.TarContainer 0.000s 38 calls diffoscope.comparators.xz.XzContainer 0.000s 24 calls diffoscope.comparators.deb.DebContainer 0.000s 8 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 1.466s) 1.463s 1 call html 0.002s 1 call text 0.001s 1 call json ## recognizes (total time: 5.658s) 1.888s 3524 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 1.773s 12 calls diffoscope.comparators.binary.FilesystemFile 1.663s 1880 calls diffoscope.comparators.utils.archive.ArchiveMember 0.333s 972 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.439s) 0.439s 156 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 46.500s CPU time consumed: 57.499s Tue Dec 17 21:37:16 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Tue Dec 17 21:37:16 UTC 2024 E: rdkit failed to build reproducibly in unstable on amd64. Tue Dec 17 21:37:18 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Dec 17 21:37:18 UTC 2024 I: Submitting 20K b1/rdkit_202409.2-2_amd64.buildinfo.asc Tue Dec 17 21:37:19 UTC 2024 I: Submitting 20K b2/rdkit_202409.2-2_amd64.buildinfo.asc Tue Dec 17 21:37:20 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Dec 17 21:37:20 UTC 2024 I: Done submitting .buildinfo files. Tue Dec 17 21:37:20 UTC 2024 I: Removing signed rdkit_202409.2-2_amd64.buildinfo.asc files: removed './b1/rdkit_202409.2-2_amd64.buildinfo.asc' removed './b2/rdkit_202409.2-2_amd64.buildinfo.asc'