Tue Nov 5 12:58:58 UTC 2024 I: starting to build rdkit/unstable/amd64 on jenkins on '2024-11-05 12:58' Tue Nov 5 12:58:58 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/23674/console.log Tue Nov 5 12:58:58 UTC 2024 I: Downloading source for unstable/rdkit=202309.3-7 --2024-11-05 12:58:58-- http://deb.debian.org/debian/pool/main/r/rdkit/rdkit_202309.3-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2959 (2.9K) [text/prs.lines.tag] Saving to: ‘rdkit_202309.3-7.dsc’ 0K .. 100% 294M=0s 2024-11-05 12:58:58 (294 MB/s) - ‘rdkit_202309.3-7.dsc’ saved [2959/2959] Tue Nov 5 12:58:58 UTC 2024 I: rdkit_202309.3-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rdkit Binary: python3-rdkit, rdkit-doc, rdkit-data, librdkit1t64, librdkit-dev, postgresql-17-rdkit Architecture: any all Version: 202309.3-7 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-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-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: 6441bee2cdbc2a1ee07d32fb6e1422f71b91a6ee 61897848 rdkit_202309.3.orig.tar.xz a368e2de2697d4da0eb16dc3c91f50d82acb3352 25152 rdkit_202309.3-7.debian.tar.xz Checksums-Sha256: 59f424979d8f2773337ab99605dea4ab4cadbd6c7fd4598fe263d6c19de7a14c 61897848 rdkit_202309.3.orig.tar.xz 29a71eeaf809318e1069132e80dff6495a00136b435e8bba016d4969d0bf10ad 25152 rdkit_202309.3-7.debian.tar.xz Files: 9414102f1ecf8a2a3f62bf46b95f65a7 61897848 rdkit_202309.3.orig.tar.xz 45df243fefe8a519ac9cbfebddd677a2 25152 rdkit_202309.3-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmbxTAUSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHW0MP/RfWeEZjeV1HRoBkROry5/i/zd5klNVY 3mColF7NTUMnL4wIZEUqvaVXos4N450jDoJ+wYL3J/3/fTEwZ/9ufXe0V1HH7bRb ATn8/D7YI7eMW8tsdriKx7BdjwnEVX9xNpMFIhlF6fw0VVHqB6geNQJxSMIJrIeD D1GtGnr94URHbesCLD++D/z79JzQhJRU4xaEOfSBHCdPtVZwTFxDRhJt+vOBg/9p OAXp7gVI3jObyP3R26cuTeQdiBt3bJaBHtE6d1LL9I5Kvkg1UMbJYe1h5e8QJQpC W6l+fpOMnPkc4y+4tPq5KZeiwt888aqieGLSm8oYUYMCg5sL2xE4trwHm40oVvmB mGzUkF0ja6uC+OmdSuvm5ACOUsnesgOZFKufCH644jpuw5bSz0Umbaz9bFsD/ODd gFBh64SA5JBhFRq3NNAjnyaeOydOhrE6A1v/KiwmKFdy2iEC/iMhLZy/KXpvfjR/ TG+SFNFWruLwnv7BLOJNg0IzCbaYCehk9N0zrXy8//5aNjSUqRKBJzjDyyFnLFrt w+Y0nVcoTkvarYCOWKS+qotse05+S4Qiw9gP0PjuK4QTzPfEd45B7sc6meub7sEe SR4Ck2wVGdQjKG+KqaTwXvpTVIsaqUL1DdbWOP+zBoZAdqaNQotfvt8syRahgTPM Grep/Sfd+Zb8 =bBbR -----END PGP SIGNATURE----- Tue Nov 5 12:58:58 UTC 2024 I: Checking whether the package is not for us Tue Nov 5 12:58:58 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Nov 5 12:58:58 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Nov 5 13:16:21 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 8 07:22:02 -12 2025 I: pbuilder-time-stamp: 1765221722 I: 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_202309.3-7.dsc] I: copying [./rdkit_202309.3.orig.tar.xz] I: copying [./rdkit_202309.3-7.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Sep 23 11:07:49 2024 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rdkit_202309.3-7.dsc: no acceptable signature found dpkg-source: info: extracting rdkit in rdkit-202309.3 dpkg-source: info: unpacking rdkit_202309.3.orig.tar.xz dpkg-source: info: unpacking rdkit_202309.3-7.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 pg16 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3055525/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='844c266ba2184b74888b3a1693936e66' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3055525' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/pbuilderrc_kGTZ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/b1 --logfile b1/build.log rdkit_202309.3-7.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3055525/tmp/hooks/D02_print_environment finished -> 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-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-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 ... 19968 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-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-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-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-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-pygments{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, 360 newly installed, 0 to remove and 0 not upgraded. Need to get 413 MB of archives. After unpacking 2106 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 [781 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-2 [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 1.19.1-1 [11.1 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 1.19.1-1 [14.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.1-1 [490 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 2.82.2-2 [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 1:1.1.2-3+b2 [24.4 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 2:1.8.10-1 [337 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-1 [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+really2.9.14-0.1 [699 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 imagemagick-7-common all 8:7.1.1.39+dfsg1-2 [66.7 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libmagickcore-7.q16-10 amd64 8:7.1.1.39+dfsg1-2 [1844 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libmagickwand-7.q16-10 amd64 8:7.1.1.39+dfsg1-2 [339 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 265 [36.4 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 sensible-utils all 0.0.24 [24.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 postgresql-common all 265 [169 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-1 [814 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-1 [2162 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 62 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-1 [1965 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-1 [671 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 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 0.22.5-2 [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 1.23.0-5 [1181 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-10 [97.2 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 0.22.5-2 [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 4.8.12-3.2 [7771 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.3-1 [26.0 MB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.3-1 [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 14.2.0-8 [42.5 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libobjc-14-dev amd64 14.2.0-8 [170 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libclang-common-19-dev amd64 1:19.1.3-1 [739 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 llvm-19-linker-tools amd64 1:19.1.3-1 [1262 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.3-1 [7616 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 clang-19 amd64 1:19.1.3-1 [115 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.30.5-1 [2223 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 8.10.1-2 [352 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-2 [81.6 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 1.48.0-6 [148 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.30.5-1 [11.4 MB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 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 0.22.5-2 [1601 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 13.20 [915 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 3.20.2-1 [10.3 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 6.20241024 [109 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 2.82.2-2 [138 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 girepository-tools amd64 2.82.2-2 [144 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+dfsg1-2 [726 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 imagemagick amd64 8:7.1.1.39+dfsg1-2 [19.8 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 0.42.2-1+b1 [556 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+b2 [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 10.0.1-1 [477 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-3+b1 [35.6 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 1.1.3-4.1 [75.5 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20241102-1 [22.7 MB] Get: 185 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20241102-1 [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 3.12.0-3+b1 [152 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.2-10 [47.0 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libblkid-dev amd64 2.40.2-10 [203 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3.2 [10.6 MB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-3.2 [235 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-3.2 [240 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-3.2 [230 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-3.2 [333 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-3.2 [372 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-3.2 [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 1.83.0-3.2 [329 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 1.83.0-3.2 [346 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-3.2 [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 1.83.0-3.2 [306 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-1 [2149 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.3-2 [157 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-1 [5122 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-1 [505 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-3.2 [327 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 219 http://deb.debian.org/debian unstable/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get: 220 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-3.2 [230 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-3.2 [231 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 223 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2 [269 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-3.2 [276 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 226 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b5 [316 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libcairo-script-interpreter2 amd64 1.18.2-2 [58.8 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.44-2 [366 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-1.1+b1 [414 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.7-1 [370 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b2 [249 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.42-4+b2 [237 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.42-4+b2 [55.8 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.42-4+b2 [763 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.7-3 [160 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libmount-dev amd64 2.40.2-10 [28.8 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libsysprof-capture-4-dev amd64 47.0-2 [47.6 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev amd64 2.82.2-2 [1674 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libglib2.0-data all 2.82.2-2 [1274 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libglib2.0-bin amd64 2.82.2-2 [126 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev-bin amd64 2.82.2-2 [162 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.82.2-2 [51.1 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev amd64 2.82.2-2 [51.8 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libpixman-1-dev amd64 0.42.2-1+b1 [573 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 257 http://deb.debian.org/debian unstable/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3+b2 [40.8 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-1 [890 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libxcb-render0-dev amd64 1.17.0-2+b1 [118 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0-dev amd64 1.17.0-2+b1 [108 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b2 [104 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b2 [35.8 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libcairo2-dev amd64 1.18.2-2 [43.0 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libcoordgen3 amd64 3.0.2-1+b2 [225 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libcoordgen-dev amd64 3.0.2-1+b2 [46.9 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libinchi1.07 amd64 1.07.1+dfsg-4 [556 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libinchi-dev amd64 1.07.1+dfsg-4 [19.4 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.6-3+b2 [147 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libmaeparser1 amd64 1.3.1-1+b2 [94.0 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libmaeparser-dev amd64 1.3.1-1+b2 [13.7 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git83-g91970fe-1 [368 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libpq5 amd64 17.0-1+b2 [220 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libpq-dev amd64 17.0-1+b2 [145 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 librsvg2-2 amd64 2.59.1+dfsg-1 [1860 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 librsvg2-bin amd64 2.59.1+dfsg-1 [2006 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.1 [794 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libz3-dev amd64 4.8.12-3.2 [90.7 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 llvm-19-runtime amd64 1:19.1.3-1 [549 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 llvm-19 amd64 1:19.1.3-1 [16.4 MB] Get: 311 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1 [134 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 llvm-19-tools amd64 1:19.1.3-1 [510 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 llvm-19-dev amd64 1:19.1.3-1 [43.2 MB] Get: 315 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get: 317 http://deb.debian.org/debian unstable/main amd64 postgresql-client-17 amd64 17.0-1+b2 [1999 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 postgresql-server-dev-17 amd64 17.0-1+b2 [1310 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 postgresql-server-dev-all amd64 265 [20.7 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 326 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1 [118 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 python3-commonmark all 0.9.1-6 [45.3 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 python3-greenlet amd64 3.1.0-1 [165 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 336 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get: 339 http://deb.debian.org/debian unstable/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 python3-mdit-py-plugins all 0.4.2-1 [32.4 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.4.7-4 [731 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.4.7-4 [588 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 python3-myst-parser all 4.0.0-1 [78.7 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [4389 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.4.0-1 [502 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 python3-sqlalchemy all 2.0.32+ds1-1 [1196 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 tex-gyre all 20180621-6 [6209 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2024.20241102-1 [4991 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20241102-1 [8757 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20241102-1 [17.0 MB] Get: 360 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20241102-1 [24.6 MB] Fetched 413 MB in 9s (43.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19968 files and directories currently installed.) 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_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.10-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../03-libexpat1_2.6.3-2_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../04-libbrotli1_1.1.0-2+b5_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b5) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../05-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... 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_1.19.1-1_amd64.deb ... Unpacking libheif-plugin-libde265:amd64 (1.19.1-1) ... Selecting previously unselected package libheif1:amd64. Preparing to unpack .../16-libheif1_1.19.1-1_amd64.deb ... Unpacking libheif1:amd64 (1.19.1-1) ... 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_2.82.2-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-2) ... 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%3a1.1.2-3+b2_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b2) ... 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%3a1.8.10-1_all.deb ... Unpacking libx11-data (2:1.8.10-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../35-libx11-6_2%3a1.8.10-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-1) ... 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. Preparing to unpack .../37-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../38-libxml2_2.12.7+dfsg+really2.9.14-0.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package imagemagick-7-common. Preparing to unpack .../39-imagemagick-7-common_8%3a7.1.1.39+dfsg1-2_all.deb ... Unpacking imagemagick-7-common (8:7.1.1.39+dfsg1-2) ... Selecting previously unselected package libmagickcore-7.q16-10:amd64. Preparing to unpack .../40-libmagickcore-7.q16-10_8%3a7.1.1.39+dfsg1-2_amd64.deb ... Unpacking libmagickcore-7.q16-10:amd64 (8:7.1.1.39+dfsg1-2) ... Selecting previously unselected package libmagickwand-7.q16-10:amd64. Preparing to unpack .../41-libmagickwand-7.q16-10_8%3a7.1.1.39+dfsg1-2_amd64.deb ... Unpacking libmagickwand-7.q16-10:amd64 (8:7.1.1.39+dfsg1-2) ... Selecting previously unselected package libjson-perl. 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_265_all.deb ... Unpacking postgresql-client-common (265) ... 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 sensible-utils. Preparing to unpack .../49-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package ucf. Preparing to unpack .../50-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package postgresql-common. Preparing to unpack .../51-postgresql-common_265_all.deb ... Adding 'diversion of /usr/bin/pg_config to /usr/bin/pg_config.libpq-dev by postgresql-common' Unpacking postgresql-common (265) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../52-libpython3.12-minimal_3.12.7-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../53-python3.12-minimal_3.12.7-1_amd64.deb ... Unpacking python3.12-minimal (3.12.7-1) ... Setting up libpython3.12-minimal:amd64 (3.12.7-1) ... Setting up libexpat1:amd64 (2.6.3-2) ... Setting up python3.12-minimal (3.12.7-1) ... 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 ... 22094 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... 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-3_all.deb ... Unpacking tzdata (2024b-3) ... 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_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... 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_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-5_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 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../14-libpython3.12-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../15-python3.12_3.12.7-1_amd64.deb ... Unpacking python3.12 (3.12.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../16-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 23149 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... 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Setting up libblkid-dev:amd64 (2.40.2-10) ... Setting up libllvm19:amd64 (1:19.1.3-1) ... Setting up catch2 (3.7.1-0.4) ... Setting up libz3-dev:amd64 (4.8.12-3.2) ... 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-4) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... 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 (0.22.5-2) ... Setting up libclang1-19 (1:19.1.3-1) ... 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 (1.83.0-3.2) ... Setting up libxpm4:amd64 (1:3.5.17-1+b2) ... Setting up libpcre2-dev:amd64 (10.42-4+b2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libice-dev:amd64 (2:1.1.1-1) ... Setting up libtool (2.4.7-8) ... Setting up libgirepository-2.0-0:amd64 (2.82.2-2) ... Setting up libselinux1-dev:amd64 (3.7-3) ... 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 (1.6.44-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-3.2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libglib2.0-bin (2.82.2-2) ... Setting up libobjc4:amd64 (14.2.0-8) ... Setting up libobjc-14-dev:amd64 (14.2.0-8) ... 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 (1:1.1.2-3+b2) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... 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 (1.83.0-3.2) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up shared-mime-info (2.4-5+b1) ... 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 (1.83.0-3.2) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Setting up llvm-19-linker-tools (1:19.1.3-1) ... 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 (1:19.1.3-1) ... 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 (2.40.2-10) ... Setting up libclang-cpp19 (1:19.1.3-1) ... Setting up libboost-thread1.83-dev:amd64 (1.83.0-3.2) ... 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 (2.82.2-2) ... Setting up girepository-tools:amd64 (2.82.2-2) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.10.1-2) ... 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 (1.83.0-3.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpq5:amd64 (17.0-1+b2) ... Setting up libx11-dev:amd64 (2:1.8.10-1) ... Setting up libpq-dev (17.0-1+b2) ... 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 (1:19.1.3-1) ... 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 (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up postgresql-common (265) ... 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 (3.30.5-1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up llvm-19 (1:19.1.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b2) ... Setting up tex-gyre (20180621-6) ... Setting up libboost-thread-dev:amd64 (1.83.0.2+b2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+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 (3.12.7-1) ... Setting up postgresql-client-17 (17.0-1+b2) ... 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 (3.12.7-1) ... Setting up debhelper (13.20) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up librsvg2-2:amd64 (2.59.1+dfsg-1) ... Setting up libpython3.12t64:amd64 (3.12.7-1) ... 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 (2024.20241102-1) ... 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 (3.12.6-1) ... Setting up librsvg2-bin (2.59.1+dfsg-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.7-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-pil:amd64 (10.4.0-1) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up texlive-latex-base (2024.20241102-1) ... 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 (2024.20241102-1) ... Setting up python3-greenlet (3.1.0-1) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.7-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up texlive-pictures (2024.20241102-1) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-markdown-it (3.0.0-2) ... Setting up texlive-fonts-recommended (2024.20241102-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-commonmark (0.9.1-6) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libgio-2.0-dev-bin (2.82.2-2) ... Setting up libpython3-dev:amd64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.4.0-1) ... 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) ... Setting up texlive-latex-extra (2024.20241102-1) ... 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 (3.12.6-1) ... Setting up libboost-python1.83-dev (1.83.0-3.2) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up libglib2.0-dev-bin (2.82.2-2) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-babel (2.14.0-1) ... 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 (2.82.2-2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up libcairo2-dev:amd64 (1.18.2-2) ... Setting up llvm-19-tools (1:19.1.3-1) ... Setting up dh-python (6.20241024) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up llvm-19-dev (1:19.1.3-1) ... Setting up postgresql-server-dev-17 (17.0-1+b2) ... Setting up postgresql-server-dev-all:amd64 (265) ... Setting up libheif-plugin-dav1d:amd64 (1.19.1-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.1-1) ... Setting up libheif1:amd64 (1.19.1-1) ... Setting up libmagickcore-7.q16-10:amd64 (8:7.1.1.39+dfsg1-2) ... Setting up libmagickwand-7.q16-10:amd64 (8:7.1.1.39+dfsg1-2) ... Setting up imagemagick-7.q16 (8:7.1.1.39+dfsg1-2) ... 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+dfsg1-2) ... Processing triggers for libc-bin (2.40-3) ... 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 (7.4.7-4) ... 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... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/rdkit-202309.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202309.3-7_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202309.3-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys 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-202309.3' find /build/reproducible-path/rdkit-202309.3 -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 pg_buildext clean /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit build-%v rm -rf build-*/ make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' 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-202309.3' 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 -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -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 -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -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 CMake Warning (dev) at CMakeLists.txt:293 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" 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. -- Found PythonInterp: /usr/bin/python3.12 (found version "3.12.7") CMake Warning (dev) at CMakeLists.txt:302 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" 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. -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.12.so (found version "3.12.7") CMake Warning (dev) at Code/cmake/Modules/FindNumPy.cmake:10 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:317 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at Code/cmake/Modules/FindNumPy.cmake:14 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): CMakeLists.txt:317 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:331 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" 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. CMake Warning (dev) at CMakeLists.txt:331 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" 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. CMake Warning at /usr/share/cmake-3.30/Modules/FindBoost.cmake:2250 (message): No header defined for python-py312; skipping header check (note: header-only libraries have no designated component) Call Stack (most recent call first): CMakeLists.txt:331 (find_package) CMake Warning (dev) at CMakeLists.txt:331 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" 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. CMake Warning (dev) at CMakeLists.txt:331 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" 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. Python Install directory /usr/lib/python3.12/site-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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 CMake Warning (dev) at CMakeLists.txt:452 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" 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. -- Found Boost: /usr/include (found suitable version "1.83.0", minimum required is "1.58.0") found components: system serialization iostreams regex CMake Warning (dev) at CMakeLists.txt:462 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" 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. -- Found Boost: /usr/include (found suitable version "1.83.0", minimum required is "1.58.0") found components: system iostreams regex == Using strict rotor definition -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/x86_64-linux-gnu/libmaeparser.so' -- Found maeparser: /usr/include -- coordgen include dir set as /usr/include -- coordgen libraries set as '/usr/lib/x86_64-linux-gnu/libcoordgen.so' -- Found coordgen: /usr/include CMake Warning (dev) at Code/GraphMol/FilterCatalog/CMakeLists.txt:5 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" 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. -- 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") CMake Warning (dev) at Code/GraphMol/RGroupDecomposition/CMakeLists.txt:26 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" 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. -- Could NOT find Boost (missing: program_options) (found suitable version "1.83.0", minimum required is "1.58.0") -- Configuring done (1.5s) -- Generating done (1.2s) CMake Warning: Manually-specified variables were not used by the project: 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 -- Build files have been written to: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_build cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/cmake 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy 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make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o [ 0%] Built target coordgen_support [ 0%] Built target ringdecomposerlib_support [ 0%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o [ 0%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o [ 0%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.cpp [ 0%] Building CXX object 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o -MF CMakeFiles/RDGeneral.dir/types.cpp.o.d -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ 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CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/ga/StringChromosome.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/ga/Chromosome.cpp [ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o [ 3%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDStreams/streams.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/ga/BinaryStringChromosomePolicy.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/catch_main.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202309.3/External/GA/ga/IntegerStringChromosomePolicy.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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-202309.3/Code/RDGeneral/LocaleSwitcher.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/util/RandomUtil.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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-202309.3/Code/RDGeneral/versions.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh/hcdriver.c [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o [ 3%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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-202309.3/Code/RDGeneral/RDLog.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/util/Util.cpp [ 3%] Built target inchi_support [ 3%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2023.09.3 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2023.09.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 3%] Built target hc [ 3%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2023.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so [ 3%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2023.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so /usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 3%] Built target ga /usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 3%] Built target rdkitCatch [ 3%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2023.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 3%] Built target RDStreams [ 3%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o 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Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs 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Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/ExplicitBitVect.cpp [ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testConcurrentQueue.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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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/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-202309.3/Code/Catalogs/Catalog.cpp [ 5%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogParams.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.cpp [ 5%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_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 -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/catch_logs.cpp [ 5%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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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/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-202309.3/Code/DataStructs/BitVect.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testDict.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseBitVect.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteValueVect.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.cpp [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/FPBReader.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/MaxMinPicker.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 6%] Linking CXX executable testMatCalc cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Built target SimDivPickers [ 7%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/testPickers.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Built target testConcurrentQueue cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Built target EigenSolvers [ 7%] Linking CXX executable logTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Built target logTestsCatch [ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Built target testMatrices [ 7%] Linking CXX executable testQuery cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 7%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2023.09.3 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so 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"Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs 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/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make -f 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/catch_tests.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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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 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/testFPB.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/testDatastructs.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.cpp cd 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Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o [ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o [ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 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Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp [ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o [ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp [ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp [ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_Utils.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 12%] Built target dictTestsCatch [ 12%] Linking CXX executable testRDValue cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 12%] Built target testRDValue [ 12%] Linking CXX executable testDict cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 [ 13%] Linking CXX executable pickersTestsCatch cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 13%] Built target pickersTestsCatch [ 13%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 13%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o [ 13%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202309.3/Code/Geometry/testGrid.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/AlignPoints.cpp [ 13%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/catch_tests.cpp [ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o [ 14%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o [ 14%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o [ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o [ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp [ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o [ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/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-202309.3/Code/Geometry/testTransforms.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Bond.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/testConrec.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryBond.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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-202309.3/Code/Geometry/Wrap/UniformGrid3D.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp cd 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryAtom.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && 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CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AtomIterators.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 15%] Built target InfoTheory [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/BondIterators.cpp make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp [ 16%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 190 | python::def("BulkDiceSimilarity", &BulkDice>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | "return the Dice similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here 219 | wrapOne("IntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:200:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 200 | python::def("BulkTanimotoSimilarity", | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | &BulkTanimoto>, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | "return the Tanimoto similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here 219 | wrapOne("IntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 211 | python::def("BulkTverskySimilarity", &BulkTversky>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 | (python::args("v1"), python::args("v2"), python::args("a"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 | python::args("b"), python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 | "return the Tversky similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here 219 | wrapOne("IntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long int]' 190 | python::def("BulkDiceSimilarity", &BulkDice>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | "return the Dice similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:220:28: required from here 220 | wrapOne("LongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:200:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long int]' 200 | python::def("BulkTanimotoSimilarity", | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | &BulkTanimoto>, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | "return the Tanimoto similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:220:28: required from here 220 | wrapOne("LongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long int]' 211 | python::def("BulkTverskySimilarity", &BulkTversky>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 | (python::args("v1"), python::args("v2"), python::args("a"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 | python::args("b"), python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 | "return the Tversky similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:220:28: required from here 220 | wrapOne("LongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' 190 | python::def("BulkDiceSimilarity", &BulkDice>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | "return the Dice similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:221:27: required from here 221 | wrapOne("UIntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:200:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' 200 | python::def("BulkTanimotoSimilarity", | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | &BulkTanimoto>, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | "return the Tanimoto similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:221:27: required from here 221 | wrapOne("UIntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = unsigned int]' 211 | python::def("BulkTverskySimilarity", &BulkTversky>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 | (python::args("v1"), python::args("v2"), python::args("a"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 | python::args("b"), python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 | "return the Tversky similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:221:27: required from here 221 | wrapOne("UIntSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long unsigned int]' 190 | python::def("BulkDiceSimilarity", &BulkDice>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | "return the Dice similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:222:29: required from here 222 | wrapOne("ULongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:200:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long unsigned int]' 200 | python::def("BulkTanimotoSimilarity", | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | &BulkTanimoto>, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 | (python::args("v1"), python::args("v2"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 | python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | "return the Tanimoto similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:222:29: required from here 222 | wrapOne("ULongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long unsigned int]' 211 | python::def("BulkTverskySimilarity", &BulkTversky>, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 | (python::args("v1"), python::args("v2"), python::args("a"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 | python::args("b"), python::args("returnDistance") = false), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 | "return the Tversky similarities between one vector and a " | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | "sequence of others"); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:222:29: required from here 222 | wrapOne("ULongSparseIntVect"); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/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-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ [ 16%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp [ 16%] Linking CXX executable testFPB cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -MF CMakeFiles/GraphMol.dir/Aromaticity.cpp.o.d -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Aromaticity.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 16%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so [ 16%] Built target testFPB make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/Data /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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-202309.3/Code/ML/Data/cQuantize.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 16%] Built target Clustering [ 16%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2023.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ConjugHybrid.cpp [ 16%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 16%] Built target Alignment [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AddHs.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 16%] Built target ChemicalFeatures 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/testAlignment.cpp [ 16%] Linking CXX executable testMultiFPB cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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&mol) { | ~~~~~~~~~~~~~^~~ [ 16%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 16%] Built target testMultiFPB [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Matrices.cpp [ 16%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd 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-DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 17%] Built target geometryTestsCatch [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -MF CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o.d -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/testChemicalFeatures.cpp [ 17%] Linking CXX executable testTransforms cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 19%] Built target testChemicalFeatures [ 20%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o 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cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 20%] Built target testDataStructs [ 21%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 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../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 21%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/MolTransforms/MolTransforms.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o 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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/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerParams.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/Subgraphs.cpp [ 23%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o [ 23%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o [ 23%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd 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Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdqueries.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/CIPLabeler/CIPMol.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -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-202309.3/Code/GraphMol/SmilesParse/smiles.tab.cpp cd 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-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-202309.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Writer.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Queries.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/lex.yysln.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o [ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/sln.tab.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o cd 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-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-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o cd 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-std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp [ 25%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 25%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd 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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 -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 25%] Built target MolCatalog make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp [ 26%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 26%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 26%] Built target Trajectory make -f 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Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdTrajectory.cpp [ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.cpp [ 27%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Trajectory.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o [ 27%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/LinearSearch.cpp [ 27%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 27%] Built target Subgraphs [ 28%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 28%] Built target rdChemicalFeatures [ 28%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2023.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 28%] Built target Optimizer make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/BondStretch.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/ForceField/MMFF/Params.cpp [ 31%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 31%] Built target GenericGroups make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 31%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o [ 32%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.cpp [ 32%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 32%] Built target MolTransforms make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 32%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o [ 32%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o [ 32%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp [ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 33%] Built target rdPartialCharges [ 34%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2023.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/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-202309.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 34%] Linking CXX executable testOptimizer cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Built target testOptimizer [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so 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rdBase [ 34%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Built target rdtrajectory [ 34%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Built target rdMolCatalog [ 34%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Built target rdqueries [ 34%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2023.09.3 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Built target ForceField [ 34%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Built target MolInterchange make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Built target rdSLNParse [ 34%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 34%] Built target SmilesParse make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/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-202309.3/Code/GraphMol/memtest1.cpp [ 36%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_queries.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/test1.cpp [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 36%] Built target rdMolTransforms [ 36%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 36%] Built target SubstructMatch make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make -f 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o [ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o [ 37%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o [ 37%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o [ 37%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp [ 37%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o [ 37%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp [ 37%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o [ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -MF CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o.d -o CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_moliterators.cpp [ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o [ 37%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o [ 37%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o [ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o [ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp [ 37%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o [ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o [ 38%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o [ 38%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp [ 39%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/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-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp [ 39%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/querytest.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/SmilesParse/smatest.cpp [ 39%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o [ 39%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o [ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp [ 39%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o [ 40%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/test.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp [ 40%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o [ 40%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 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CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.cpp [ 43%] Linking CXX executable graphmolMemTest1 cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so 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-ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 43%] Built target graphmolMemTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 43%] Built target rdShapeHelpers [ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp [ 43%] Linking CXX executable queryTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 43%] Built target graphmolIterTest [ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 43%] Built target queryTestsCatch [ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp [ 43%] Linking CXX executable graphmolcpTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 43%] Built target rdMolInterchange [ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 43%] Built target graphmolcpTest [ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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[ 44%] Linking CXX executable moliteratorTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 [ 44%] Built target testSubgraphs2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/ReducedGraphs/test1.cpp [ 44%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target Abbreviations make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp [ 44%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so [ 44%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 44%] Built target MolAlign 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-202309.3/obj-x86_64-linux-gnu' make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -MF CMakeFiles/Depictor.dir/RDDepictor.cpp.o.d -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp [ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Templates.cpp [ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o [ 44%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap/rdCoordGen.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp [ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so [ 44%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target FragCatalog cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target ForceFieldHelpers make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make -f 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o [ 44%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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-202309.3/Code/ForceField/Wrap/ForceField.cpp [ 44%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp [ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistGeomUtils.cpp [ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o [ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o [ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/TriangleSmooth.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralViolationContrib.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistViolationContrib.cpp [ 44%] Linking CXX executable testReducedGraphs cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target testReducedGraphs [ 44%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target FilterCatalog make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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-c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 44%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp [ 44%] Linking CXX executable graphmolqueryTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target graphmolqueryTest [ 44%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target rdReducedGraphs cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target MolChemicalFeatures make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o [ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp [ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o [ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 44%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2023.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target Fingerprints make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o [ 44%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::UFFConfsHelper(ROMol&, int, int, double, bool)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: warning: redundant move in return statement [-Wredundant-move] 49 | return std::move(pyres); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: note: remove 'std::move' call /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::MMFFConfsHelper(ROMol&, int, int, std::string, double, bool)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: warning: redundant move in return statement [-Wredundant-move] 66 | return std::move(pyres); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: note: remove 'std::move' call /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::FFConfsHelper(ROMol&, ForceFields::PyForceField&, int, int)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: warning: redundant move in return statement [-Wredundant-move] 86 | return std::move(pyres); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: note: remove 'std::move' call [ 45%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2023.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 45%] Linking CXX executable testSLNParse cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Built target DistGeometry make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build 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-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o [ 45%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o [ 45%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/DistGeom.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp [ 45%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/testDistGeom.cpp [ 45%] Built target testSLNParse /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp: In function 'boost::python::api::object RDKit::GetAtomMatch(boost::python::api::object, int)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: warning: redundant move in return statement [-Wredundant-move] 45 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: note: remove 'std::move' call [ 45%] Linking CXX executable smaTest1 cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitPathsHelper(const RDKit::AdditionalOutput&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: warning: redundant move in return statement [-Wredundant-move] 452 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: note: remove 'std::move' call /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitInfoMapHelper(const RDKit::AdditionalOutput&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: warning: redundant move in return statement [-Wredundant-move] 467 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: note: remove 'std::move' call make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Built target smaTest1 [ 45%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Built target rdCoordGen [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Built target rdForceFieldHelpers [ 45%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Built target testDistGeom [ 45%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Built target O3AAlign [ 45%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2023.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Built target Depictor make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make -f 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/build make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o [ 45%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o [ 46%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o [ 46%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDInchiLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDINCHILIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o -MF CMakeFiles/RDInchiLib.dir/inchi.cpp.o.d -o CMakeFiles/RDInchiLib.dir/inchi.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/INCHI-API/inchi.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 46%] Built target rdAbbreviations [ 47%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target DistGeom [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 47%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target rdMolChemicalFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target rdForceField [ 47%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target DistGeomHelpers [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target rdMHFPFingerprint [ 47%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2023.09.3 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' [ 47%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdinchi_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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-202309.3/External/INCHI-API/Wrap/pyInchi.cpp [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target rdDepictor [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target rdFingerprintGenerator [ 47%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target ChemTransforms 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f 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-DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PDBSupplier.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PDBWriter.cpp [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.cpp [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -MF CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o.d -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceWriters.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PNGParser.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SVGParser.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK 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CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp [ 50%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 50%] Built target rdinchi [ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 50%] Built target rdfiltercatalog [ 50%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2023.09.3 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o 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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.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 50%] Built target FileParsers make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/CoordGen 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"--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.cpp [ 51%] Building CXX object 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -MF CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o.d -o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.cpp [ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o cd 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 56%] Built target graphmolOrganometallicsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 56%] Built target molBundleTest [ 56%] Linking CXX executable testSequence cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 [ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp [ 56%] Linking CXX executable nontetrahedralCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 [ 56%] Linking CXX executable hanoiTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 56%] Linking CXX executable pickleTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 56%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 56%] Built target hanoiTest make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake 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Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/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-202309.3/Code/GraphMol/FileParsers/connectTheDots_catch.cpp 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 57%] Built target graphmoltestPicklerGlobalSetting make -f 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/Substruct/catch_tests.cpp [ 57%] Built target pickleTestsCatch make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" [ 58%] Linking CXX executable graphmolSGroupCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -MF CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o.d -o CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/generic_tests.cpp [ 58%] Linking CXX executable testCoordGen cd 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 59%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Built target testUFFForceField make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Built target testExtendedStereoParsing make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/test1.cpp make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp [ 59%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 59%] Linking CXX executable graphmolAdjustQueryCatch cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Built target graphmolAdjustQueryCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp [ 59%] Linking CXX executable cxsmilesTest cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp: In function 'void testMostSubstitutedCoreMatch()': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(orthoMeta.std::unique_ptr::get(), 0)' 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:60: note: the temporary was destroyed at the end of the full expression 'std::make_pair(ortho.std::unique_ptr::get(), 1)' 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(meta.std::unique_ptr::get(), 1)' 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:55: note: the temporary was destroyed at the end of the full expression 'std::make_pair(biphenyl.std::unique_ptr::get(), 2)' 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { | ^ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(phenyl.std::unique_ptr::get(), 3)' 1903 | std::make_pair(phenyl.get(), 3u)}) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ [ 60%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 60%] Linking CXX executable connectTheDotsTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 60%] Built target connectTheDotsTest make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 60%] Linking CXX executable testSGroup cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 60%] Built target testSGroup make -f 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 60%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 [ 60%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o [ 60%] Linking CXX executable testMolWriter cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF 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/usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/MolAlign/catch_tests.cpp [ 60%] Linking CXX executable graphmolTest1 cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 61%] Linking CXX executable testFragCatalog cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp [ 61%] Linking CXX executable molfileStereoCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 61%] Linking CXX executable filterCatalogTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 61%] Built target molfileStereoCatchTest make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/FMCS.cpp [ 61%] Linking CXX executable cdxmlParserCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/MMPA/MMPA.cpp [ 61%] Linking CXX executable testMMFFForceField cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -MF CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/catch_tests.cpp [ 61%] Linking CXX executable testMolTransforms cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 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CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp [ 61%] Linking CXX executable substructTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 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/usr/lib/x86_64-linux-gnu/libmaeparser.so [ 61%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so [ 63%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/CIPLabeler/Mancude.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 63%] Built target rdfragcatalog [ 63%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.cpp [ 64%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread 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/usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 64%] Linking CXX executable testPropertyLists cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 [ 64%] Linking CXX executable graphmoltestPickler /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 [ 64%] Linking CXX executable fpGenTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so 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../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 64%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 64%] Built target testCrystalForceField [ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 64%] Built target testPropertyLists make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 64%] Built target graphmoltestPickler [ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp [ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -MF CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/PartitionSet.cpp [ 65%] Built target fpGenTestCatch 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/trajectoryTest.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 65%] Built target graphmoltestChirality make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/test1.cpp [ 65%] Linking CXX executable depictorCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 65%] Built target depictorCatch [ 65%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 65%] Linking CXX executable testShapeHelpers cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 66%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 66%] Built target testMMFFForceFieldHelpers [ 66%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Linking CXX executable fpTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 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66%] Linking CXX executable testFeatures [ 66%] Built target fpTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 67%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 67%] Built target testChemTransforms make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 67%] Built target chemTransformsTestCatch [ 67%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2023.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 67%] Built target MMPA make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp [ 67%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 67%] Linking CXX executable distGeomHelpersCatch cd /build/reproducible-path/rdkit-202309.3/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 67%] Built target distGeomHelpersCatch [ 68%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 68%] Linking CXX executable testFingerprintGenerators cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 68%] Built target trajectoryTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 68%] Built target testFingerprintGenerators [ 68%] Linking CXX executable smiTest1 cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 68%] Linking CXX executable testUFFForceFieldHelpers cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 68%] Built target smiTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 68%] Built target testUFFForceFieldHelpers [ 69%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 69%] Built target rdDistGeom [ 69%] Linking CXX executable smiTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 69%] Built target smiTestCatch [ 69%] Linking CXX executable testCIPLabeler cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 69%] Built target testCIPLabeler [ 69%] Linking CXX executable molInterchangeTest1 cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 69%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 69%] Built target graphmolTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 69%] Built target Descriptors make -f External/INCHI-API/CMakeFiles/testInchi.dir/build.make External/INCHI-API/CMakeFiles/testInchi.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/INCHI-API 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"--color=" make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 71%] Built target testMMPA [ 71%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/MoleculeParser.cpp [ 71%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd 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../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 71%] Linking CXX executable molInterchangeCatchTest cd 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../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 72%] Linking CXX executable testDistGeomHelpers cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 72%] Built target FMCS make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend [ 72%] Built target testDistGeomHelpers make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 72%] Built target molInterchangeCatchTest make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/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-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp [ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 72%] Built target rdMMPA [ 72%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp [ 72%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp [ 72%] Linking CXX executable testAbbreviations cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 73%] Linking CXX executable testCoulombMat cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 /usr/bin/c++ -g 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../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/mces_catch.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c 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../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 73%] Linking CXX executable testWHIM cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 73%] Linking CXX executable testEEM [ 73%] Built target testMORSE cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 73%] Linking CXX executable testGETAWAY cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 73%] Built target testWHIM make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 73%] Built target testEEM [ 73%] Linking CXX executable testRDF cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 73%] Built target testGETAWAY [ 74%] Linking CXX executable testAUTOCORR3D cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 74%] Linking CXX executable testAUTOCORR2D cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Built target testRDF make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Built target testAUTOCORR3D make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Built target testAUTOCORR2D [ 74%] Linking CXX executable fileParsersCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp: In function 'boost::python::api::object {anonymous}::degenerateSmartsQueryMolDictHelper(const RDKit::MCSResult&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: warning: redundant move in return statement [-Wredundant-move] 646 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: note: remove 'std::move' call [ 74%] Linking CXX executable testPBF cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPBF.dir/testPBF.cpp.o -o testPBF ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Built target testPBF make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Built target fileParsersCatchTest [ 74%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2023.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 74%] Linking CXX executable testRDFcustom cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2023.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Built target MolHash make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 74%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/catch_tests.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Built target testRDFcustom [ 74%] Linking CXX executable testMolAlign cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 74%] Built target testMolAlign [ 75%] Linking CXX executable descriptorsTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 75%] Built target descriptorsTestCatch [ 75%] Linking CXX executable test3D cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 75%] Built target test3D [ 76%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target FMCStest [ 76%] Linking CXX executable testInchi cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/testInchi.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testInchi.dir/test.cpp.o -o testInchi ../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../lib/libRDKitDescriptors.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 76%] Linking CXX executable testO3AAlign cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target testInchi make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target testO3AAlign [ 76%] Linking CXX executable testRascalCluster cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target testRascalCluster [ 76%] Linking CXX executable fileParsersTest1 cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target fileParsersTest1 [ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target rdMolHash [ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target rdMolAlign make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target rdRascalMCES [ 76%] Linking CXX executable molHashCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target molHashCatchTest [ 76%] Linking CXX executable testDescriptors cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 76%] Built target testDescriptors [ 77%] Linking CXX executable testRascalMCES cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 77%] Built target rdFMCS [ 77%] Built target testRascalMCES [ 77%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 77%] Linking CXX executable testFMCS cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 77%] Built target testFMCS [ 77%] 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 Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make[4]: Entering directory 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/MolStandardize.cpp [ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/Deprotect/Deprotect.cpp [ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o [ 80%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp [ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp [ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinWriter.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/PositionVariation.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdmolops.cpp [ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.cpp [ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o [ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o [ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Validate.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/LinkNode.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ChiralityOps.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.cpp [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o [ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o [ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp [ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o [ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Charge.cpp [ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Fragment.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp [ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/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-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/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-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp [ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp [ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp [ 82%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so [ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp [ 83%] Building CXX object 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../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/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-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp [ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2023.09.3 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 83%] Built target Deprotect [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/deprotectTest.cpp [ 83%] Linking CXX executable testReactionFingerprints cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 83%] Built target testReactionFingerprints make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp In file included from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', 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-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:113:32: /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/list:63, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:16: 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-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:113:32: /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))); | ^ [ 83%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp [ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 83%] Built target rdMolDescriptors [ 83%] Linking CXX executable testEnumeration cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 83%] Built target testEnumeration [ 83%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 83%] Built target MolEnumerator make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o [ 83%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp [ 84%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o 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../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so [ 84%] Linking CXX executable deprotectTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 84%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 86%] Built target deprotectTest [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 86%] Built target rdDeprotect [ 86%] Linking CXX executable molValidateTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 87%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 87%] Built target molValidateTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 87%] Built target MarvinParser make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/RingInfo.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Wrap/SDWriter.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTWriter.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 89%] Built target molFragmentTest [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/PDBWriter.cpp [ 89%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /build/reproducible-path/rdkit-202309.3/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o 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/usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libcairo.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 89%] Built target MolDraw2D make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp [ 89%] Linking CXX executable molStandardizeSmallTest cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 89%] Built target molStandardizeSmallTest make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp [ 90%] Linking CXX executable molNormalizeTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 90%] Built target molNormalizeTest make -f 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp [ 90%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 90%] Built target ScaffoldNetwork [ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp [ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/EditableMol.cpp [ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MonomerInfo.cpp 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/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-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp [ 93%] Linking CXX executable molChargeTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp [ 93%] Built target molChargeTest make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 94%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp [ 94%] Linking CXX executable rxnTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so 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/usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 94%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 94%] Built target rxnTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 94%] Built target TautomerQuery make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -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-202309.3/Code/GraphMol/TautomerQuery/catch_tests.cpp [ 94%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 94%] Built target rdMolEnumerator make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 94%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp [ 94%] Linking CXX executable molStandardizeTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp [ 97%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp [ 98%] Linking CXX executable molTautomerTest cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 98%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Linking CXX executable testMolEnumerator cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 [ 98%] Built target molStandardizeCatchTest /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 98%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Built target testMolEnumerator make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Built target rdMolStandardize make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Built target rdmolops [ 98%] Linking CXX executable tautomerQueryTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Built target tautomerQueryTestCatch 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-202309.3/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-202309.3/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-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-202309.3/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-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-202309.3/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-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-202309.3/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-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Linking CXX executable testScaffoldNetwork cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Built target testScaffoldNetwork [ 98%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Built target rdScaffoldNetwork [ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Built target rdTautomerQuery [ 98%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 98%] Built target GeneralizedSubstruct make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o [ 99%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp [ 99%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt 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Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make 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Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/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.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 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/usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target rdmolfiles [ 99%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target moldraw2DTest1 [ 99%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 99%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 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99%] Built target testRGroupDecompInternals make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target rdchem [ 99%] Linking CXX executable generalizedSubstructCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 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../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target rdGeneralizedSubstruct [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target rdChemReactions [ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target rdMolDraw2D [ 99%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target rgroupCatchTests [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitga.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target rdRGroupDecomposition [ 99%] Linking CXX executable testReaction cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target testReaction [ 99%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target SubstructLibrary make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [100%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [100%] Built target moldraw2DTestCatch [100%] Linking CXX executable testRGroupDecomp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [100%] Built target testRGroupDecomp [100%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [100%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [100%] Built target substructLibraryCatchTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [100%] Built target substructLibraryTest [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [100%] Built target rdSubstructLibrary make[3]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' STATIC_LINK=0 RDKIT_LIBDIR=/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//lib pg_buildext build /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit build-%v ### PostgreSQL 17 build ### make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/build-17' gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rdkit_io.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_io.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o mol_op.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_murckoscaffold': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:406:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 406 | CROMol scaffold = MolMurckoScaffold(mol); | ^~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_nm_hash': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:426:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 426 | char *str = computeNMMolHash(mol, opts); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:428:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 428 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:421:7: warning: unused variable 'len' [-Wunused-variable] 421 | int len; | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_adjust_query_properties': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:441:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 441 | char *data = PG_GETARG_CSTRING(1); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:447:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 447 | Mol *res = deconstructROMolWithQueryProperties(adj); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_to_svg': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:462:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 462 | char *legend = PG_GETARG_CSTRING(1); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_to_xqmol': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:482:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 482 | bool doEnumeration = PG_GETARG_BOOL(1); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:493:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 493 | XQMol *res = deconstructXQMol(xqm); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:512:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 512 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol2s_transition': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:580:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 580 | text *ts = (text *)palloc(ts_size); // new return value | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:600:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 600 | char *smiles = makeMolText(mol, &len, false, false); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mols': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:638:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 638 | int32 ts_size = VARHDRSZ + strlen(str); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles_transition': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:544:1: warning: control reaches end of non-void function [-Wreturn-type] 544 | } | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol_transition': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:679:1: warning: control reaches end of non-void function [-Wreturn-type] 679 | } | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_op.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o sfp_op.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/sfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rxn_op.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c:134:3: warning: multi-line comment [-Wcomment] 134 | // /* keep compiler quiet - no extra ; */ \ | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c: In function 'reaction_to_svg': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c:149:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 149 | bool highlightByReactants = PG_GETARG_BOOL(1); | ^~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rdkit_gist.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldistsign': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:219:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 219 | uint8 *as = (uint8 *)VARDATA(a); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldist': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:238:10: warning: unused variable 'd' [-Wunused-variable] 238 | double d; | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gmol_consistent': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:484:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 484 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:496:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 496 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:526:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 526 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gmol_cmp': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:555:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 555 | int siglen = SIGLEN(a); | ^~~ In file included from /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit.h:44, from /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:40: /usr/include/postgresql/17/server/varatt.h:244:68: warning: pointer targets in passing argument 2 of 'bitstringGrayCmp' differ in signedness [-Wpointer-sign] 244 | #define VARDATA_4B(PTR) (((varattrib_4b *) (PTR))->va_4byte.va_data) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ | | | char * /usr/include/postgresql/17/server/varatt.h:278:65: note: in expansion of macro 'VARDATA_4B' 278 | #define VARDATA(PTR) VARDATA_4B(PTR) | ^~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:41: note: in expansion of macro 'VARDATA' 558 | int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); | ^~~~~~~ In file included from /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:43: /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.h:60:41: note: expected 'uint8 *' {aka 'unsigned char *'} but argument is of type 'char *' 60 | int bitstringGrayCmp(int length, uint8 *bstr1, uint8 *bstr2); | ~~~~~~~^~~~~ /usr/include/postgresql/17/server/varatt.h:244:68: warning: pointer targets in passing argument 3 of 'bitstringGrayCmp' differ in signedness [-Wpointer-sign] 244 | #define VARDATA_4B(PTR) (((varattrib_4b *) (PTR))->va_4byte.va_data) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ | | | char * /usr/include/postgresql/17/server/varatt.h:278:65: note: in expansion of macro 'VARDATA_4B' 278 | #define VARDATA(PTR) VARDATA_4B(PTR) | ^~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:53: note: in expansion of macro 'VARDATA' 558 | int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); | ^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.h:60:55: note: expected 'uint8 *' {aka 'unsigned char *'} but argument is of type 'char *' 60 | int bitstringGrayCmp(int length, uint8 *bstr1, uint8 *bstr2); | ~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 558 | int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'rdkit_consistent': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:643:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 643 | int siglen = SIGLEN(query); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:657:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 657 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gsfp_consistent': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:689:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 689 | int sum, overlapSum, overlapN; | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:693:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 693 | int nKey = (ISALLTRUE(key)) | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'greaction_consistent': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:757:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 757 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:774:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 774 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:800:9: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 800 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c: At top level: /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:631:13: warning: 'rdkit_consistent' defined but not used [-Wunused-function] 631 | static bool rdkit_consistent(GISTENTRY *entry, StrategyNumber strategy, | ^~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:237:12: warning: 'soergeldist' defined but not used [-Wunused-function] 237 | static int soergeldist(bytea *a, bytea *b) { | ^~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_gist.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c: In function 'gbfp_cmp': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c:659:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 659 | GBfp *gbfp2 = (GBfp *)PG_DETOAST_DATUM(y); | ^~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c:662:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 662 | int siglen = GBFP_LEAF_SIGLEN(gbfp1); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c:665:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 665 | int retval = bitstringGrayCmp(siglen, GET_LEAF_DATA(gbfp1)->fp, GET_LEAF_DATA(gbfp2)->fp); | ^~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c: In function 'merge_key': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c:689:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 689 | int siglen = GBFP_INNER_SIGLEN(result); | ^~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_gin.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gin.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o low_gist.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/low_gist.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o guc.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/guc.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o cache.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/cache.c g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o adapter.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/adapter.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bitstring.o /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringUnion': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c:64:7: warning: unused variable 'i' [-Wunused-variable] 64 | int i; | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringIntersection': /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c:96:7: warning: unused variable 'i' [-Wunused-variable] 96 | int i; | ^ g++ -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wshadow=compatible-local -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fno-omit-frame-pointer -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -shared -o rdkit.so rdkit_io.o mol_op.o bfp_op.o sfp_op.o rxn_op.o rdkit_gist.o bfp_gist.o bfp_gin.o low_gist.o guc.o cache.o adapter.o bitstring.o -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/llvm-19/lib -Wl,--as-needed -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -L/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//lib -lRDKitGeneralizedSubstruct -lRDKitMolEnumerator -lRDKitTautomerQuery -lRDKitMolDraw2D -lRDKitMolTransforms -lRDKitMolHash -lRDKitFMCS -lRDKitChemReactions -lRDKitChemTransforms -lRDKitFileParsers -lRDKitSmilesParse -lRDKitFingerprints -lRDKitSubgraphs -lRDKitDescriptors -lRDKitPartialCharges -lRDKitSubstructMatch -lRDKitGraphMol -lRDKitEigenSolvers -lRDKitDataStructs -lRDKitDepictor -lRDKitRDGeometryLib -lRDKitRDGeneral -pthread sed -e's/@RDKIT_PG_MOL_GIST_SORTSUPPORT@/FUNCTION 11 gmol_sortsupport (internal),/' \ -e's/@RDKIT_PG_QMOL_GIST_SORTSUPPORT@/FUNCTION 11 gmol_sortsupport (internal),/' \ -e's/@RDKIT_PG_BFP_GIST_SORTSUPPORT@/FUNCTION 11 gbfp_sortsupport (internal),/' \ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit.sql.in > rdkit--4.4.0.sql /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rdkit_io.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_io.c /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o mol_op.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:544:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 544 | } | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/mol_op.c:679:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 679 | } | ^ 2 warnings generated. /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_op.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_op.c /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o sfp_op.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/sfp_op.c /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rxn_op.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c:100:37: warning: passing arguments to 'ReactionSubstructFP' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 100 | PG_RETURN_BOOL(ReactionSubstructFP(rxn, rxn2)); | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rxn_op.c:115:37: warning: passing arguments to 'ReactionSubstructFP' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 115 | PG_RETURN_BOOL(ReactionSubstructFP(rxn2, rxn)); | ^ 2 warnings generated. /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rdkit_gist.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:41: warning: passing 'char[]' to parameter of type 'uint8 *' (aka 'unsigned char *') converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign] 558 | int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); | ^~~~~~~~~~ /usr/include/postgresql/17/server/varatt.h:278:27: note: expanded from macro 'VARDATA' 278 | #define VARDATA(PTR) VARDATA_4B(PTR) | ^~~~~~~~~~~~~~~ /usr/include/postgresql/17/server/varatt.h:244:26: note: expanded from macro 'VARDATA_4B' 244 | #define VARDATA_4B(PTR) (((varattrib_4b *) (PTR))->va_4byte.va_data) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.h:60:41: note: passing argument to parameter 'bstr1' here 60 | int bitstringGrayCmp(int length, uint8 *bstr1, uint8 *bstr2); | ^ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit_gist.c:558:53: warning: passing 'char[]' to parameter of type 'uint8 *' (aka 'unsigned char *') converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign] 558 | int retval = bitstringGrayCmp(siglen, VARDATA(a), VARDATA(b)); | ^~~~~~~~~~ /usr/include/postgresql/17/server/varatt.h:278:27: note: expanded from macro 'VARDATA' 278 | #define VARDATA(PTR) VARDATA_4B(PTR) | ^~~~~~~~~~~~~~~ /usr/include/postgresql/17/server/varatt.h:244:26: note: expanded from macro 'VARDATA_4B' 244 | #define VARDATA_4B(PTR) (((varattrib_4b *) (PTR))->va_4byte.va_data) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.h:60:55: note: passing argument to parameter 'bstr2' here 60 | int bitstringGrayCmp(int length, uint8 *bstr1, uint8 *bstr2); | ^ 2 warnings generated. /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_gist.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gist.c /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_gin.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bfp_gin.c /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o low_gist.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/low_gist.c /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o guc.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/guc.c /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o cache.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/cache.c /usr/bin/clang-19 -std=c++17 -xc++ -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -emit-llvm -c -o adapter.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/adapter.cpp /usr/lib/llvm-19/bin/opt -module-summary -f adapter.bc -o adapter.bc /usr/bin/clang-19 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -Wno-format-truncation -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202309.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit -I/usr/include/postgresql/17/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bitstring.bc /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/bitstring.c make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/build-17' ### End 17 build ### (cd /build/reproducible-path/rdkit-202309.3/Code; doxygen doxygen/doxygen.config) warning: Tag 'TCL_SUBST' at line 213 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 '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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Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AtomIterators.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AtomIterators.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Bond.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Bond.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/BondIterators.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/BondIterators.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... 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Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/PreprocessRxn.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/PreprocessRxn.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionPickler.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionPickler.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Descriptor.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Descriptor.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Priority.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Priority.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Pairlist.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4c.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5New.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule6.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule6.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rules.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rules.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/TooManyNodesException.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Templates.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Templates.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/TemplateSmiles.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/TemplateSmiles.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Deprotect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Deprotect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AtomFeat.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AtomFeat.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR2D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR2D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR3D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/CoulombMat.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/CoulombMat.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Crippen.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/details.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/details.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DetermineBonds/DetermineBonds.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DetermineBonds/DetermineBonds.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/GeneralFileReader.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/GeneralFileReader.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupWriting.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupWriting.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PNGParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PNGParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Graph.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Seed.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Target.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Target.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GraphMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GraphMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolBundle.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolBundle.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Graph/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:233: warning: unbalanced grouping commands Mol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/AtomSymbol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/AtomSymbol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextJS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextJS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDr/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:440: warning: unbalanced grouping commands /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:692: warning: unbalanced grouping commands aw2D/MolDraw2DDetails.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/StringRect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/StringRect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/LinkNode.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/LinkNode.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/mf.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/mf.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/MolHash.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/nmmolhash.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/nmmolhash.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/details.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryAtom.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryAtom.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryBond.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryBond.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/PartitionSet.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/PartitionSet.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalClusterOptions.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalDetails.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalDetails.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalOptions.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalOptions.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalResult.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalResult.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitQueries.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitQueries.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Resonance.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Resonance.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition//build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:416: warning: unbalanced grouping commands RGroupDecompParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Rings.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Rings.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SanitException.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SanitException.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/detail.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/detail.h... 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Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/primes.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/primes.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StereoGroup.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StereoGroup.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Stereo.h... 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Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/TautomerQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/TautomerQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogParams.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/base64.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/base64.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVects.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVects.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVectUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVectUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DatastructsException.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DatastructsException.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DatastructsStreamOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DatastructsStreamOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteValueVect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteValueVect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/ExplicitBitVect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/ExplicitBitVect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/FPBReader.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/FPBReader.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/MultiFPBReader.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/MultiFPBReader.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseBitVect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseBitVect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/AndQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/AndQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/EqualityQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/EqualityQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/GreaterEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/GreaterEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/GreaterQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/GreaterQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/LessEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/LessEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/LessQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/LessQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/NullQueryAlgebra.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/NullQueryAlgebra.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/OrQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/OrQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/Query.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/Query.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/RangeQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/RangeQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Query/XOrQuery.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Query/XOrQuery.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/CorrMatGenerator.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/CorrMatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoGainFuncs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoGainFuncs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/DistPicker.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/DistPicker.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/LeaderPicker.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/LeaderPicker.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/MaxMinPicker.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BadFileException.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BadFileException.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BoostEndInclude.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BoostEndInclude.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BoostStartInclude.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BoostStartInclude.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/ConcurrentQueue.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/ConcurrentQueue.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Exceptions.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Exceptions.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/export.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/export.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/FileParseException.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/FileParseException.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/hanoiSort.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/hanoiSort.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/LocaleSwitcher.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Ranking.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Ranking.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDAny.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDAny.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDConfig.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDConfig.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDExportMacros.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDExportMacros.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDThreads.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDThreads.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDValue.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDValue.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/StreamOps.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/StreamOps.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/versions.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/versions.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDBoost/boost_numpy.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDBoost/boost_numpy.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDBoost/import_array.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDBoost/import_array.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDBoost/pyint_api.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDBoost/pyint_api.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DistGeom/BoundsMatrix.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DistGeom/BoundsMatrix.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralSet.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralSet.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralViolationContrib.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralViolationContrib.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistGeomUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistGeomUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistViolationContrib.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistViolationContrib.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DistGeom/FourthDimContrib.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DistGeom/FourthDimContrib.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/DistGeom/TriangleSmooth.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/DistGeom/TriangleSmooth.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/Contrib.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/Contrib.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/OopBend.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/OopBend.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Matrix.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Matrix.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/SquareMatrix.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/SquareMatrix.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/SymmMatrix.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/SymmMatrix.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Numerics/Vector.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Numerics/Vector.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Grid3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Grid3D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.h... Pr/build/reproducible-path/rdkit-202309.3/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-202309.3/Code/GraphMol/MolOps.h:1082: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:1098: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined. /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:93: 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 81 of file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRows &rgr, const std::string &prefix="")' at line 85 of file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h 'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupColumn &rgr, const std::string &prefix="")' at line 89 of file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' eprocessing /build/reproducible-path/rdkit-202309.3/Code/Geometry/Utils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Geometry/Utils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/Features/Feature.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/Features/Feature.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202309.3/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 DistGeomUtils.h... Generating code for file DistViolationContrib.h... Generating code for file FourthDimContrib.h... Generating code for file TriangleSmooth.h... Generating code for file Feature.h... Generating code for file Contrib.h... Generating code for file ForceField.h... Generating code for file OopBend.h... Generating code for file StretchBend.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 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 Inversion.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 TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.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 Utils.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 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 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 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 details.h... Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... Generating code for file CDXMLParser.h... Generating code for file FileParsers.h... Generating code for file FileParserUtils.h... Generating code for file GeneralFileReader.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 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 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 MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.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 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 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 Tautomer.h... Generating code for file Tautomer.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... 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 LocaleSwitcher.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 f/build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.h:188: warning: found at different nesting level (7) than expected (4) /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.h:189: warning: end of comment block while expecting command or 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 DistGeomUtils.h... Generating docs for file DistViolationContrib.h... Generating docs for file FourthDimContrib.h... Generating docs for file TriangleSmooth.h... Generating docs for file Feature.h... Generating docs for file Contrib.h... Generating docs for file ForceField.h... Generating docs for file OopBend.h... Generating docs for file StretchBend.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 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 Inversion.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 TorsionAngle.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.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 Utils.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 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 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 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 details.h... Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... Generating docs for file CDXMLParser.h... Generating docs for file FileParsers.h... Generating docs for file FileParserUtils.h... Generating docs for file GeneralFileReader.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 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... Generating docs for file SequenceParsers.h... Generating docs for file SequenceWriters.h... Generating docs for file FilterCatalog.h... Generating docs for file FilterCatalogEntry.h... Generating docs for file FilterMatcherBase.h... Generating docs for file FilterMatchers.h... Generating docs for file Filters.h... Generating docs for file FunctionalGroupHierarchy.h... Generating docs for file AtomPairGenerator.h... Generating docs for file AtomPairs.h... Generating docs for file FingerprintGenerator.h... Generating docs for file Fingerprints.h... Generating docs for file FingerprintUtil.h... Generating docs for file MACCS.h... Generating docs for file MHFP.h... Generating docs for file MorganFingerprints.h... Generating docs for file MorganGenerator.h... Generating docs for file RDKitFPGenerator.h... Generating docs for file TopologicalTorsionGenerator.h... Generating docs for file Composition2N.h... Generating docs for file DebugTrace.h... 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 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... Generating docs for file FragCatGenerator.h... Generating docs for file FragCatParams.h... Generating docs for file FragFPGenerator.h... Generating docs for file XQMol.h... Generating docs for file GenericGroups.h... Generating docs for file GraphMol.h... Generating docs for file MarvinDefs.h... Generating docs for file MarvinParser.h... Generating docs for file MMPA.h... Generating docs for file AlignMolecules.h... Generating docs for file O3AAlignMolecules.h... Generating docs for file MolBundle.h... Generating docs for file MolCatalog.h... Generating docs for file MolCatalogEntry.h... Generating docs for file MolCatalogParams.h... Generating docs for file FeatureParser.h... Generating docs for file MolChemicalFeature.h... Generating docs for file MolChemicalFeatureDef.h... Generating docs for file MolChemicalFeatureFactory.h... Generating docs for file AtomSymbol.h... Generating docs for file DrawAnnotation.h... Generating docs for file DrawMol.h... Generating docs for file DrawMolMCH.h... Generating docs for file DrawMolMCHCircleAndLine.h... Generating docs for file DrawMolMCHLasso.h... Generating docs for file DrawShape.h... Generating docs for file DrawText.h... Generating docs for file DrawTextCairo.h... Generating docs for file DrawTextFT.h... Generating docs for file DrawTextFTCairo.h... Generating docs for file DrawTextFTJS.h... Generating docs for file DrawTextFTSVG.h... Generating docs for file DrawTextJS.h... Generating docs for file DrawTextNotFT.h... Generating docs for file DrawTextSVG.h... Generating docs for file roboto_regular.h... Generating docs for file telex_regular.h... Generating docs for file MolDraw2D.h... Generating docs for file MolDraw2DCairo.h... Generating docs for file MolDraw2DDetails.h... Generating docs for file MolDraw2DHelpers.h... Generating docs for file MolDraw2DJS.h... Generating 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 MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... Generating docs for file AcidBaseCatalogEntry.h... Generating docs for file AcidBaseCatalogParams.h... Generating docs for file AcidBaseCatalogUtils.h... Generating docs for file Charge.h... Generating docs for file Fragment.h... Generating docs for file FragmentCatalogEntry.h... Generating docs for file FragmentCatalogParams.h... Generating docs for file FragmentCatalogUtils.h... Generating docs for file Metal.h... Generating docs for file MolStandardize.h... Generating docs for file Normalize.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... Generating docs for file TransformCatalogEntry.h... Generating docs for file TransformCatalogParams.h... Generating docs for file TransformCatalogUtils.h... Generating docs for file Validate.h... 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 do/build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' cs for file QueryBond.h... 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 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 Tautomer.h... Generating docs for file Tautomer.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... 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... G/build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistGeomUtils.h:95: 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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: The following parameters of ForceFields::MMFF::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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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' enerating 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_adaptbx::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::DistViolationContrib... Generating docs for compound DistGeom::FourthDimContrib... Generating docs for namespace ForceFields Generating docs for compound ForceFields::ForceField... Generating docs for compound ForceFields::ForceFieldContrib... 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 namespace ForceFields::MMFF Generating docs for compound ForceFields::MMFF::AngleBendContrib... Generating docs for compound ForceFields::MMFF::AngleConstraintContrib... Generating docs for compound ForceFields::MMFF::BondStretchContrib... Generating docs for compound ForceFields::MMFF::DistanceConstraintContrib... 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 ForceField/build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.h:29: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::MMFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: The following parameters of ForceFields::UFF::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-202309.3/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-202309.3/Code/ForceField/UFF/PositionConstraint.h:29: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::UFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) s::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 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::PositionConstraintContrib... Generating docs for compound ForceFields::MMFF::StretchBendContrib... Generating docs for compound ForceFields::MMFF::TorsionAngleContrib... Generating docs for compound ForceFields::MMFF::TorsionConstraintContrib... 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::AngleConstraintContrib... Generating docs for compound ForceFields::UFF::AtomicParams... Generating docs for compound ForceFields::UFF::BondStretchContrib... Generating docs for compound ForceFields::UFF::DistanceConstraintContrib... Generating docs for compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::PositionConstraintContrib... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::TorsionConstraintContrib... 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 name/build/reproducible-path/rdkit-202309.3/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-202309.3/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' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.h:267: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.h:42: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.h:42: warning: The following parameter of RDKit::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h:51: warning: argument 'line' from the argument list of RDKit::MolDataStreamToMol has multiple @param documentation sections /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h:167: 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-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h:216: warning: The following parameter of RDKit::MolToCXSmiles(const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) is not documented: parameter 'doRandom' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h:341: 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-202309.3/Code/GraphMol/FileParsers/FileParsers.h:341: 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-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h:107: warning: The following parameter of RDKit::MolToSmiles(const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) is not documented: parameter 'doRandom' /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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' space 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 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 RD/build/reproducible-path/rdkit-202309.3/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 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: 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-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: 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-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 is not documented: parameter 'matchVect' Kit::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::ForwardSDMolSupplier... Generating docs for compound RDKit::FPBReader... Generating docs for compound RDKit::FPHolderBase... Generating 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::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::/build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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' /build/reproducible-path/rdkit-202309.3/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-202309.3/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 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' 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::MolFileUnhandledFeatureException... 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::MolSupplier... Generating docs for compound RDKit::MolWriter... Generating docs for compound RDKit::MolzipParams... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::PatternHolder... Generating docs for compound RDKit::PDBMolSupplier... Generating docs for compound RDKit::PDBWriter... Generating docs for compound RDKit::PeriodicTable... Generating docs for compound RDKit::QueryAtom... Generating docs for compound RDKit::QueryAtomIterator_... 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::RingInfo... Generating docs for compound RDKit::ROMol... Generating docs for compound RDKit::RWMol... Generating docs for compound RDKit::RxnSanitizeException... Generating docs for compound RDKit::SDMolSupplier... Generating docs for compound RDKit::SDWriter... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::SmartsParserParams... Generating docs for compound RDKit::SmilesMolSupplier... Generating docs for compound RDKit::SmilesParseException... Generating docs for compound RDKit::SmilesParserParams... 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::Substr/build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/Code/GraphMol/Fingerprints/AtomPairs.h:95: 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-202309.3/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-202309.3/Code/GraphMol/Canon.h:103: 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' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h:138: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented: parameter 'flagPossible' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h:190: warning: The following parameter of RDKit::Chirality::getTrigonalBipyramidalAxialBond(const Atom *center, int which=0) is not documented: parameter 'center' /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/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' uctLibrary... Generating docs for compound RDKit::SubstructMatchParameters... Generating docs for compound RDKit::TautomerPatternHolder... Generating docs for compound RDKit::TautomerQuery... Generating docs for compound RDKit::TDTMolSupplier... 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::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... Generating 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 namespace RDKit::Chirality::detail Generating docs for namespace RDKit::CIPLabeler 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.../build/reproducible-path/rdkit-202309.3/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-202309.3/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 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: 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-202309.3/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 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: 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-202309.3/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 101 in file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.h:102: warning: found tag without matching /build/reproducible-path/rdkit-202309.3/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-202309.3/Code/GraphMol/Fingerprints/MHFP.h:141: warning: found tag without matching /build/reproducible-path/rdkit-202309.3/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-202309.3/Code/GraphMol/Fingerprints/MHFP.h:191: warning: found tag without matching /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h:148: 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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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' Generating docs for compound RDKit::Descriptors::CrippenParams... 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::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::FMCS::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::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::DrawMolMCHCi/build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:21: 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-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:21: 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' /build/reproducible-path/rdkit-202309.3/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-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/Code/GraphMol/MolOps.h:801: warning: The following parameter of RDKit::MolOps::getAdjacencyMatrix(const ROMol &mol, bool useBO=false, int emptyVal=0, bool force=false, const char *propNamePrefix=nullptr, const boost::dynamic_bitset<> *bondsToUse=nullptr) is not documented: parameter 'bondsToUse' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.h:281: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) are not documented: parameter 'mergeUnmappedOnly' parameter 'mergeIsotopes' rcleAndLine... 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 RDKit::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::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::RemoveHsParameters... Generating docs for namespace RDKit::MolOps::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::DisallowedAtomsValidation... 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::IsotopeValidation... Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser... Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKi/build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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' t::MolStandardize::MetalDisconnectorOptions... Generating docs for compound RDKit::MolStandardize::MolVSValidation... Generating docs for compound RDKit::MolStandardize::MolVSValidations... 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::RDKitValidation... Generating docs for compound RDKit::MolStandardize::Reionizer... 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::ValidationErrorInfo... Generating docs for compound RDKit::MolStandardize::ValidationMethod... Generating docs for namespace RDKit::MolStandardize::defaults 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 R/build/reproducible-path/rdkit-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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-202309.3/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 DKit::SLNParse::AttribType... Generating docs for namespace RDKit::SmartsWrite Generating docs for namespace RDKit::SmilesWrite Generating docs for namespace RDKit::SmilesWrite::detail Generating docs 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 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 33474/65536 hits=200051 misses=37090 symbol lookup cache used 29448/65536 hits=269122 misses=29448 finished... (cd /build/reproducible-path/rdkit-202309.3/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202309.3 /usr/bin/make html) make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202309.3/Code/docs/* _build/html/cppapi cp -r C++Examples _build/html/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v7.4.7 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 308 source files that are out of date updating environment: [new config] 308 added, 0 changed, 0 removed reading sources... 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Contiguous Rotatable Bonds ========================= /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:7: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cartridge.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:10: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cartridge.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:2501: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cartridge.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md:3: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md:305: WARNING: duplicate label writing molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:358: WARNING: Explicit markup ends without a blank line; unexpected unindent. /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:12: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:30: WARNING: duplicate label reading single molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:104: WARNING: duplicate label reading sets of molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:208: WARNING: duplicate label writing molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:390: WARNING: duplicate label writing sets of molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:431: WARNING: duplicate label working with molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:435: WARNING: duplicate label looping over atoms and bonds, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:478: WARNING: duplicate label ring information, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:547: WARNING: duplicate label modifying molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:615: WARNING: duplicate label working with 2d molecules: generating depictions, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:665: WARNING: duplicate label working with 3d molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:788: WARNING: duplicate label preserving molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:844: WARNING: duplicate label drawing molecules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:1083: WARNING: duplicate label substructure searching, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:1148: WARNING: duplicate label stereochemistry in substructure matches, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:1186: WARNING: duplicate label atom map indices in smarts, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:3425: WARNING: duplicate label the sssr problem, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst:3829: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md.rst:226: WARNING: Non-consecutive header level increase; H4 to H6 /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md:450: WARNING: duplicate label recommended extras, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md:494: WARNING: duplicate label testing the build (optional, but recommended), other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md:499: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/Overview.md:145: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:1563: ERROR: Malformed table. Text in column margin in table line 15. ======================== ========= Alkyl (ALK) alkyl side chains (not an H atom) AlkylH (ALH) alkyl side chains including an H atom Alkenyl (AEL) alkenyl side chains AlkenylH (AEH) alkenyl side chains or an H atom Alkynyl (AYL) alkynyl side chains AlkynylH (AYH) alkynyl side chains or an H atom Alkoxy (AOX) alkoxy side chains AlkoxyH (AOH) alkoxy side chains or an H atom Carbocyclic (CBC) carbocyclic side chains CarbocyclicH (CBH) carbocyclic side chains or an H atom Carbocycloalkyl (CAL) cycloalkyl side chains CarbocycloalkylH (CAH) cycloalkyl side chains or an H atom Carbocycloalkenyl (CEL) cycloalkenyl side chains CarbocycloalkenylH (CEH) cycloalkenyl side chains or an H atom Carboaryl (ARY) all-carbon aryl side chains CarboarylH (ARH) all-carbon aryl side chains or an H atom Cyclic (CYC) cyclic side chains CyclicH (CYH) cyclic side chains or an H atom Acyclic(ACY) acyclic side chains (not an H atom) AcyclicH (ACH) acyclic side chains or an H atom Carboacyclic (ABC) all-carbon acyclic side chains CarboacyclicH (ABH) all-carbon acyclic side chains or an H atom Heteroacyclic (AHC) acyclic side chains with at least one heteroatom HeteroacyclicH (AHH) acyclic side chains with at least one heteroatom or an H atom Heterocyclic (CHC) cyclic side chains with at least one heteroatom HeterocyclicH (CHH) cyclic side chains with at least one heteroatom or an H atom Heteroaryl (HAR) aryl side chains with at least one heteroatom HeteroarylH (HAH) aryl side chains with at least one heteroatom or an H atom NoCarbonRing (CXX) ring containing no carbon atoms NoCarbonRingH (CXH) ring containing no carbon atoms or an H atom Group (G) any group (not H atom) GroupH (GH) any group (including H atom) Group* (G*) any group with a ring closure GroupH* (GH*) any group with a ring closure or an H atom ======================== ========= /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:1664: WARNING: Enumerated list ends without a blank line; unexpected unindent. /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:180: WARNING: duplicate label aromaticity, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:385: WARNING: duplicate label dative bonds, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:536: WARNING: duplicate label stereochemistry, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:1264: WARNING: duplicate label chemical features, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:2200: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:2298: WARNING: duplicate label rdkit fingerprints, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/GettingStartedInPython.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/RDKit_Book.rst:2464: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/Overview.md WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.rst WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Avalon.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst:113: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Avalon.rst WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Draw.rst:21: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.aggCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.cairoCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.canvasbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.mplCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.qtCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Draw.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Draw.rst WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.EState.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.EState.rst WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Features.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Features.rst WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fraggle.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Fraggle.rst WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolDb.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolDb.rst WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolStandardize.rst:6: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolKey.rst WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolStandardize.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.MolKey.rst WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Subshape.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Subshape.rst WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Suppliers.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.Suppliers.rst WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst:2: WARNING: Title underline too short. rdkit.Chem.rdForceFieldHelpers module ================================= WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolDescriptors module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolInterchange module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst:2: WARNING: Title underline too short. rdkit.Chem.rdPartialCharges module ================================= WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst:2: WARNING: Title underline too short. rdkit.Chem.rdRGroupDecomposition module ================================= WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst:2: WARNING: Title underline too short. rdkit.Chem.rdSubstructLibrary module ================================= WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.fmcs.rst WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.fmcs.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.rst WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.Metric.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.Metric.rst WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataStructs.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Dbase.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataStructs.rst WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbReport' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Dbase.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Dbase.rst WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DistanceGeometry.rst WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DistanceGeometry.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ForceField.rst WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.DataManip.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst:24: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Geometry.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst:38: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Geometry.rst WARNING: autodoc: failed to import module 'ML.AnalyzeComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.BuildComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Composite.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Cluster.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Composite.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Cluster.rst WARNING: autodoc: failed to import module 'ML.Composite.AdjustComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.BayesComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.CompositeRun' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Composite.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Composite.rst WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.DecTree.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Data.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.DecTree.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Data.rst WARNING: autodoc: failed to import module 'ML.DecTree.BuildQuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildSigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Forest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.ID3' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.PruneTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.QuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.SigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Tree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.DecTree.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.DecTree.rst WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.EnrichPlot' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.GrowComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Descriptors.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Descriptors.rst WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst:2: WARNING: Title underline too short. rdkit.ML.InfoTheory.rdInfoTheory module ====================================== WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.KNN.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.KNN.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.InfoTheory.rst WARNING: autodoc: failed to import module 'ML.KNN.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.DistFunctions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNRegressionModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.KNN.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.KNN.rst WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.ModelPackage.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.MLUtils.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.ModelPackage.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.MLUtils.rst WARNING: autodoc: failed to import module 'ML.ModelPackage.PackageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.Packager' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.ModelPackage.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.ModelPackage.rst WARNING: autodoc: failed to import module 'ML.NaiveBayes.ClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Neural.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Neural.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst WARNING: autodoc: failed to import module 'ML.Neural.ActFuncs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.NetNode' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Network' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Trainers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Neural.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Neural.rst WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.SLT.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.SLT.rst WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ScreenComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Scoring.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.Scoring.rst WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Numerics.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Numerics.rst WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.ML.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.SimDivFilters.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.SimDivFilters.rst WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.rst WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'six' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.NodeLib.rst /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.VLib.NodeLib.rst WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202309.3/Docs/Book/data/README.md: WARNING: document isn't included in any toctree /build/reproducible-path/rdkit-202309.3/Docs/Book/source/rdkit.Chem.SpacialScore.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying downloadable files... 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[100%] images/query_atoms.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 444 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/Docs/Book' # (cd /build/reproducible-path/rdkit-202309.3/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202309.3 /usr/bin/make latexpdf) make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' cp -r rdkit obj-*/ find /build/reproducible-path/rdkit-202309.3 -name rdchem.so /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202309.3 PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//lib:" PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//lib:" dh_auto_test cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/rdkit-202309.3/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: testInchi 1: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API/testInchi 1: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API 1: Test timeout computed to be: 1500 test 2 Start 2: testCoordGen 2: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/CoordGen/testCoordGen 2: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/CoordGen 2: Test timeout computed to be: 1500 test 3 Start 3: pyCoordGen 3: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap/testCoordGen.py" 3: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/CoordGen/Wrap 3: Test timeout computed to be: 1500 test 4 Start 4: testDict 4: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral/testDict 4: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral 4: Test timeout computed to be: 1500 test 5 Start 5: testRDValue 5: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral/testRDValue 5: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral 5: Test timeout computed to be: 1500 test 6 Start 6: testConcurrentQueue 6: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral/testConcurrentQueue 6: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral 6: Test timeout computed to be: 1500 test 7 Start 7: dictTestsCatch 7: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral/dictTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral 7: Test timeout computed to be: 1500 test 8 Start 8: logTestsCatch 8: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral/logTestsCatch 8: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral 8: Test timeout computed to be: 1500 test 9 Start 9: testDataStructs 9: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/testDataStructs 9: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs 9: Test timeout computed to be: 1500 test 10 Start 10: testFPB 10: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/testFPB 10: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs 10: Test timeout computed to be: 1500 test 11 Start 11: testMultiFPB 11: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/testMultiFPB 11: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs 11: Test timeout computed to be: 1500 test 12 Start 12: pyBV 12: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testBV.py" 12: Working Directory: /build/reproducible-path/rdkit-202309.3/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/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testDiscreteValueVect.py" 13: Working Directory: /build/reproducible-path/rdkit-202309.3/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/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testSparseIntVect.py" 14: Working Directory: /build/reproducible-path/rdkit-202309.3/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/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testFPB.py" 15: Working Directory: /build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu/Code/Geometry/testTransforms 16: Working Directory: /build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu/Code/Geometry/testGrid 17: Working Directory: /build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu/Code/Geometry/geometryTestsCatch 18: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry 18: Test timeout computed to be: 1500 test 19 Start 19: testPyGeometry 19: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/testGeometry.py" 19: Working Directory: /build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu/Code/Numerics/testMatrices 20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics 20: Test timeout computed to be: 1500 test 21 Start 21: testConrec 21: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/testConrec 21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics 21: Test timeout computed to be: 1500 test 22 Start 22: testAlignment 22: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment 22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment 22: Test timeout computed to be: 1500 test 23 Start 23: pyAlignment 23: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/testAlignment.py" 23: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap 23: Test timeout computed to be: 1500 test 24 Start 24: testOptimizer 24: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer 24: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer 24: Test timeout computed to be: 1500 test 25 Start 25: testUFFForceField 25: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField 25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/UFF 25: Test timeout computed to be: 1500 test 26 Start 26: testMMFFForceField 26: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField 26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF 26: Test timeout computed to be: 1500 test 27 Start 27: pyForceFieldConstraints 27: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/testConstraints.py" 27: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap 27: Test timeout computed to be: 1500 test 28 Start 28: testDistGeom 28: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom 28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom 28: Test timeout computed to be: 1500 test 29 Start 29: pyDistGeom 29: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" 29: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap 29: Test timeout computed to be: 1500 test 30 Start 30: graphmolTest1 30: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 30: Test timeout computed to be: 1500 test 31 Start 31: graphmolcpTest 31: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest 31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 31: Test timeout computed to be: 1500 test 32 Start 32: graphmolqueryTest 32: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest 32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 32: Test timeout computed to be: 1500 test 33 Start 33: graphmolMolOpsTest 33: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest 33: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 test 34 Start 34: graphmoltestChirality 34: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality 34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 test 35 Start 35: graphmoltestPickler 35: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler 35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 test 36 Start 36: graphmoltestPicklerGlobalSetting 36: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 test 37 Start 37: graphmolIterTest 37: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest 37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 test 38 Start 38: hanoiTest 38: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest 38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 38: Test timeout computed to be: 1500 test 39 Start 39: graphmolMemTest1 39: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 test 40 Start 40: resMolSupplierTest 40: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest 40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 test 41 Start 41: molBundleTest 41: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest 41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 test 42 Start 42: testSGroup 42: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup 42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 1: [07:34:57] ------------------------------------- 1: [07:34:57] ------------------------------------- 1: [07:34:57] ------------------------------------- 1: [07:34:57] ------------------------------------- 1: [07:34:57] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored 1: [07:34:57] ------------------------------------- 1: [07:34:57] ------------------------------------- 1: [07:34:57] ------------------------------------- 1: [07:34:57] Test multithreading 1: reading molecules 1: generating reference data 1: processing 1: launch :0 1: launch :1 1: launch :2 1: launch :3 2: core 2: RDKit 2D 2: 2: 4 4 0 0 0 0 0 0 0 0999 V2000 2: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 1 1 0 2: M END 2: 2: core+sidechain 2: RDKit 2D 2: 2: 7 7 0 0 0 0 0 0 0 0999 V2000 2: 0.6496 0.9080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.3926 -0.0584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4726 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.3396 -0.0616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.2048 -0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.3590 -0.3156 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.6160 0.6508 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 2 6 1 0 2: 6 7 1 0 2: 7 1 1 0 2: M END 2: 2: templated 2: RDKit 2D 2: 2: 7 7 0 0 0 0 0 0 0 0999 V2000 2: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 2 6 1 0 2: 6 7 1 0 2: 7 1 1 0 2: M END 2: 2: core 2: RDKit 2D 2: 2: 10 10 0 0 0 0 0 0 0 0999 V2000 2: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 10 1 1 0 2: M END 2: 2: core+sidechain 2: RDKit 2D 2: 2: 12 12 0 0 0 0 0 0 0 0999 V2000 2: 0.2846 -0.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.2790 -1.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5898 -2.2466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.4530 -1.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.4476 -0.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5788 -0.2468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5732 0.7532 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.2956 1.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.3012 2.2482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.1700 2.7434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.1590 0.7434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.1534 -0.2564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 8 11 1 0 2: 11 12 1 0 2: 12 1 1 0 2: M END 2: 2: templated 2: RDKit 2D 2: 2: 12 12 0 0 0 0 0 0 0 0999 V2000 2: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 8 11 1 0 2: 11 12 1 0 2: 12 1 1 0 2: M END 2: 2: core 2: RDKit 2D 2: 2: 10 10 0 0 0 0 0 0 0 0999 V2000 2: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 10 1 1 0 2: M END 2: 2: core+sidechain 2: RDKit 2D 2: 2: 16 16 0 0 0 0 0 0 0 0999 V2000 2: 1.7868 0.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.6532 1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.5187 0.7785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.5180 -0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.6515 -0.7209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.7860 -0.2201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.9195 -0.7195 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0539 -0.2189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.8124 -0.7181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.6780 -0.2175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.5445 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.4101 -0.2161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -4.2764 -0.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -5.1421 -0.2147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0547 0.7811 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.9211 1.2805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 10 11 1 0 2: 11 12 1 0 2: 12 13 1 0 2: 13 14 1 0 2: 8 15 1 0 2: 15 16 1 0 2: 16 1 1 0 2: M END 2: 2: templated 2: RDKit 2D 2: 2: 16 16 0 0 0 0 0 0 0 0999 V2000 2: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 10 11 1 0 2: 11 12 1 0 2: 12 13 1 0 2: 13 14 1 0 2: 8 15 1 0 2: 15 16 1 0 2: 16 1 1 0 2: M END 2: 2: core 2: RDKit 2D 2: 2: 9 10 0 0 0 0 0 0 0 0999 V2000 2: 0.6718 -0.9994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.5374 -0.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.5366 0.5012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.6702 1.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.1954 0.4998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.1946 -0.5002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.1454 -0.8098 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.7338 -0.0014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.1466 0.8082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 6 1 1 0 2: 9 5 1 0 2: M END 2: 2: core+sidechain 2: RDKit 2D 2: 2: 19 21 0 0 0 0 0 0 0 0999 V2000 2: -0.5657 -0.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.4321 -0.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.2977 -0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.2969 -1.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.1625 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.4329 0.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5673 1.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5681 2.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.2975 2.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2975 2.5728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.7969 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.2991 0.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.2999 -0.4278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2513 -0.7362 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.5609 -1.6870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.5393 -1.8942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.8923 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.8381 0.0734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2499 0.8820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 2 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 10 11 1 0 2: 7 12 1 0 2: 12 13 1 0 2: 13 14 1 0 2: 14 15 1 0 2: 15 16 1 0 2: 15 17 1 0 2: 14 18 1 0 2: 18 19 1 0 2: 13 1 1 0 2: 19 12 1 0 2: 11 9 1 0 2: M END 2: 2: templated 2: RDKit 2D 2: 2: 19 21 0 0 0 0 0 0 0 0999 V2000 2: 0.5360 -0.9365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.4021 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.2680 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.2680 -1.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.4020 -2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.4021 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.5360 1.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.5360 2.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.8300 3.4295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.3300 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.3300 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.2812 -0.7457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.5900 -1.6966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.9208 -2.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.5682 -1.9046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.8686 0.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.2812 0.8725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 2 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 10 11 1 0 2: 7 12 1 0 2: 12 13 1 0 2: 13 14 1 0 2: 14 15 1 0 2: 15 16 1 0 2: 15 17 1 0 2: 14 18 1 0 2: 18 19 1 0 2: 13 1 1 0 2: 19 12 1 0 2: 11 9 1 0 2: M END 2: 2: core 2: RDKit 2D 2: 2: 5 4 0 0 0 0 0 0 0 0999 V2000 2: 1.2134 -0.4976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.3444 1.0006 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5186 -0.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.3856 -0.0028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 2 4 1 0 2: 4 5 1 0 2: M END 2: 2: core+sidechain 2: RDKit 2D 2: 2: 7 6 0 0 0 0 0 0 0 0999 V2000 2: -1.7333 -0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.8661 -0.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.8641 0.9303 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.0011 -0.5713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.8659 -0.0731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.8679 0.9269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.7309 -0.5749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 2 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 5 7 1 0 2: M END 2: 2: templated 2: RDKit 2D 2: 2: 7 6 0 0 0 0 0 0 0 0999 V2000 2: 1.2227 -0.4921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.3350 1.0058 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5185 -0.5117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.3902 -0.0216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.2506 -0.5314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.4014 0.9784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 2 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 5 7 1 0 2: M END 2: 2: test1 2: RDKit 2D 2: 2: 12 12 0 0 0 0 0 0 0 0999 V2000 2: -0.2902 0.4155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.5740 0.9187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.4418 0.4219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.3060 0.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.3024 1.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.4454 -0.5781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.5812 -1.0813 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.2866 -0.5843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.1508 -1.0875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.0186 -0.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.0222 0.4095 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.8828 -1.0937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 2 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 3 6 2 0 2: 6 7 1 0 2: 7 8 2 0 2: 8 9 1 0 2: 9 10 1 0 2: 10 11 2 0 2: 10 12 1 0 2: 8 1 1 0 2: M END 2: 2: test2 2: RDKit 2D 2: 2: 5 4 0 0 0 0 0 0 0 0999 V2000 2: -0.4980 0.7210 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.0004 -0.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.8678 -0.6440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.5020 0.7182 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.8642 -0.6488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 2 4 1 0 2: 2 5 1 0 2: M END 2: 4: [07:34:57] Testing Github940: property dictionaries leaking memory 4: [07:34:57] done 4: Testing RDValue 4: Testing RDAny 4: dict set int vect 4: dict get int vect 4: static boost any:0.073907 s 5: -- running tests -- 5: min: -2147483648 -2147483648 5: min: 0 0 5: min: 2.22507e-308 2.22507e-308 5: min: 1.17549e-38 1.17549e-38 5: min: 0 0 5: == int 5: == double 5: == float 5: == unsigned int 5: == bool 5: == std::string 6: [07:34:57] 6: ----------------------------------------- 6: [07:34:57] Finished: testPushAndPop() 6: [07:34:57] 6: ----------------------------------------- 6: [07:34:57] 6: ----------------------------------------- 7: Randomness seeded to: 2700800175 7: =============================================================================== 7: All tests passed (32 assertions in 2 test cases) 7: 8: [07:34:57] should not be silent 8: [07:34:57] should not be silent 8: Randomness seeded to: 1090587886 8: [07:34:57] should not be silent 8: [07:34:57] should not be silent 8: [07:34:57] should not be silent 8: [07:34:57] should not be silent 8: [07:34:57] should not be silent 8: [07:34:57] should not be silent 8: [07:34:57] should not be silent 8: [07:34:57] should not be silent 8: =============================================================================== 8: All tests passed (26 assertions in 3 test cases) 8: 9: 10, 11, 14, 9: t1: 10, 11, 14, 9: t2: 10, 11, 15, 17, 9: t1|t2: 10, 11, 14, 15, 17, 9: t1&t2: 10, 11, 9: t1^t2: 14, 15, 17, 9: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 9: except 9: 10, 11, 14, 9: t1: 10, 11, 14, 9: t2: 10, 11, 15, 17, 9: t1|t2: 10, 11, 14, 15, 17, 9: t1&t2: 10, 11, 9: t1^t2: 14, 15, 17, 9: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 9: except 16: **************************************** 16: testPointND 16: **************************************** 16: testPointOps3D 16: **************************************** 16: testPointOps2D 16: **************************************** 16: test12D 16: ref1: 1.76094 3.98375 ref2: 3.78665 2.95704 16: pt1: 3.34199 3.4142 pt2: 4.33581 1.08962 16: **************************************** 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: **************************************** 17: *********************************************************** 17: Testing Grid 17: --------------------------------- 17: testUniformGrid1 17: 17: --------------------------------- 17: testUniformGrid2 17: 17: --------------------------------- 17: testUniformGridPickling 17: 17: --------------------------------- 17: testGridOps 17: 17: --------------------------------- 17: testUniformGridIndexing 17: 18: Randomness seeded to: 1804681434 18: =============================================================================== 18: All tests passed (50 assertions in 5 test cases) 18: 20: [07:34:57] ----------------------------------------- 20: [07:34:57] Testing RDNumerics: vectors and matrices Code 20: [07:34:57] --------------------------------------- 20: [07:34:57] test1Vector 20: [07:34:57] --------------------------------------- 20: [07:34:57] test2Matrix 20: [07:34:57] --------------------------------------- 20: [07:34:57] test3SquareMatrix 20: [07:34:57] --------------------------------------- 20: [07:34:57] test4SymmMatrix 21: Randomness seeded to: 1503316689 21: =============================================================================== 21: All tests passed (76 assertions in 3 test cases) 21: 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 25: ------------------------------------- 25: Unit tests for force field basics. 25: done 25: ------------------------------------- 25: Unit tests for basics of UFF bond-stretch terms. 25: done 25: ------------------------------------- 25: Unit tests for UFF bond-stretch terms. 25: done 25: ------------------------------------- 25: Unit tests for basics of UFF angle terms. 25: done 25: ------------------------------------- 25: Unit tests for UFF angle-bend terms. 25: theta = 3.14159; theta0 = 3.14159 25: theta = 2.094395, param1.theta0 = 2.094395 25: done 25: ------------------------------------- 25: Test Simple UFF molecule optimizations. 25: done 25: ------------------------------------- 25: Unit tests for UFF nonbonded terms. 25: done 25: ------------------------------------- 25: Test UFF torsional terms. 25: done 25: ------------------------------------- 25: Test UFF Parameter objects 25: ------------------------------------- 25: Test Simple UFF molecule optimization, part 2. 25: done 25: ------------------------------------- 25: Test UFF Torsion Conflicts. 25: C 0.4783 -0.7477 -0.0753 25: C -0.5465 -0.0176 0.3519 25: C -0.5114 1.4472 0.0870 25: H -1.5201 -0.4838 0.2485 25: H 0.4696 1.8363 0.3367 25: O -1.2618 1.9423 0.6934 25: F -0.7163 1.6298 -0.9622 25: done 25: ------------------------------------- 25: Unit tests for UFF distance constraint terms. 25: done 25: ------------------------------------- 25: Unit tests for all UFF constraint terms. 25: done 25: ------------------------------------- 25: Unit tests for copying UFF ForceFields. 26: ------------------------------------- 26: Official MMFF validation suite. 28: *********************************************************** 28: test1 28: *********************************************************** 28: testIssue216 28: Rows: 4 Columns: 4 28: 0 1 1 1 28: 1 0 1 1 28: 1 1 0 1 28: 1 1 1 0 28: *********************************************************** 28: 30: Atoms: 30: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 30: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 30: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 30: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 30: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 30: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 30: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 30: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 30: 8 22 Ti chg: 0 deg: 1 exp: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: getExplicitValence() called without call to calcExplicitValence() 30: Violation occurred on line 298 in file ./Code/GraphMol/Atom.cpp 30: Failed Expression: d_explicitValence > -1 30: **** 30: 30: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 30: Bonds: 30: 0 0->1 order: 1 conj?: 0 aromatic?: 0 30: 1 1->2 order: 2 conj?: 0 aromatic?: 0 30: 2 2->3 order: 1 conj?: 0 aromatic?: 0 30: 3 0->4 order: 1 conj?: 0 aromatic?: 0 30: 4 5->6 order: 3 conj?: 0 aromatic?: 0 30: 5 6->7 order: 1 conj?: 0 aromatic?: 0 30: 6 7->8 order: 2 conj?: 0 aromatic?: 0 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: bond already exists 30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp 30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 30: **** 30: 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: bond already exists 30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp 30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 30: **** 30: 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: attempt to add self-bond 30: Violation occurred on line 379 in file ./Code/GraphMol/RWMol.cpp 30: Failed Expression: atomIdx1 != atomIdx2 30: **** 30: 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: bond already exists 30: Violation occurred on line 441 in file ./Code/GraphMol/ROMol.cpp 30: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 30: **** 30: 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: attempt to add self-bond 30: Violation occurred on line 439 in file ./Code/GraphMol/ROMol.cpp 30: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 30: **** 30: 30: [07:34:57] Explicit valence for atom # 0 B, 4, is greater than permitted 30: [07:34:57] Explicit valence for atom # 0 B, 5, is greater than permitted 30: [07:34:57] 30: 30: **** 30: Post-condition Violation 30: Element 'Xx' not found 30: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 30: Failed Expression: anum > -1 30: **** 30: 30: [07:34:57] ------------------------------------- 30: [07:34:57] Test github381: thread-safe initialization of the periodic table 30: [07:34:57] done 30: [07:34:57] ------------------------------------- 30: [07:34:57] Test github1041: Segfault for atom with no owner (expect some warnings) 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: no owner 30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 30: Failed Expression: dp_mol 30: **** 30: 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: no owner 30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h 30: Failed Expression: dp_mol 30: **** 30: 30: [07:34:57] done 30: [07:34:57] ------------------------------------- 30: [07:34:57] Test github1041: Segfault for atom with no owner (expect some warnings) 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: no owner 30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 30: Failed Expression: dp_mol 30: **** 30: 30: [07:34:57] 30: 30: **** 30: Pre-condition Violation 30: no owner 30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h 30: Failed Expression: dp_mol 30: **** 30: 30: [07:34:57] done 30: [07:34:57] ------------------------------------- 30: [07:34:57] Test github1453: RWMol.clear() should reset the numBonds count. 30: [07:34:57] done 30: [07:34:57] ------------------------------------- 30: [07:34:57] Test range-based for loops. 30: [07:34:57] done 30: [07:34:57] ------------------------------------- 30: [07:34:57] Test github1642: Atom index type is too low for big molecules. 31: 31: 31: 31: COPY 32: [07:34:57] ---------------------- Test1 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test2 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test3 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test4 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test5 32: [07:34:57] Done! 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test issue 2892580 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test github issue 53: query molecules not matching [R] 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test queries using qualifiers instead of == 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test Github issue 165: radicals not used in atom-atom matching 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test extra atom queries 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test extra bond queries 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test num heteroatom neighbor queries 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test atom type queries 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Test Github #2471: dummy atom queries are flagged as complex 32: [07:34:57] Done! 32: [07:34:57] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() 32: [07:34:57] Done! 33: 1 1 2 33: 1 1 1 33: 2 1 0.75 33: path: 2 33: [07:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 33: [07:34:57] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored 33: [07:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 33: [07:34:57] Explicit valence for atom # 0 B, 5, is greater than permitted 33: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted 33: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted 33: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted 33: [07:34:57] Explicit valence for atom # 1 Si, 7, is greater than permitted 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing String Pickle Roundtrips. 1/223 Test #5: testRDValue ............................ Passed 0.09 sec 2/223 Test #7: dictTestsCatch ......................... Passed 0.08 sec 3/223 Test #8: logTestsCatch .......................... Passed 0.08 sec 4/223 Test #9: testDataStructs ........................ Passed 0.08 sec 5/223 Test #10: testFPB ................................ Passed 0.08 sec 6/223 Test #11: testMultiFPB ........................... Passed 0.08 sec 7/223 Test #16: testTransforms ......................... Passed 0.07 sec 8/223 Test #17: testGrid ............................... Passed 0.07 sec 9/223 Test #18: geometryTestsCatch ..................... Passed 0.07 sec 10/223 Test #20: testMatrices ........................... Passed 0.07 sec 11/223 Test #21: testConrec ............................. Passed 0.07 sec 12/223 Test #22: testAlignment .......................... Passed 0.06 sec 13/223 Test #24: testOptimizer .......................... Passed 0.06 sec 14/223 Test #28: testDistGeom ........................... Passed 0.05 sec 15/223 Test #31: graphmolcpTest ......................... Passed 0.05 sec 16/223 Test #32: graphmolqueryTest ...................... Passed 0.05 sec test 43 Start 43: test-valgrind 43: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind 43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 test 44 Start 44: graphmolTestsCatch 44: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 test 45 Start 45: graphmolOrganometallicsCatch 45: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch 45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 test 46 Start 46: graphmolSGroupCatch 46: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch 46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 test 47 Start 47: graphmolAdjustQueryCatch 47: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch 47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 47: Test timeout computed to be: 1500 test 48 Start 48: chiralityTestsCatch 48: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch 48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 test 49 Start 49: canonTestsCatch 49: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch 49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 49: Test timeout computed to be: 1500 test 50 Start 50: moliteratorTestsCatch 50: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 test 51 Start 51: queryTestsCatch 51: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 test 52 Start 52: molbundleTestsCatch 52: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 test 53 Start 53: pickleTestsCatch 53: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 test 54 Start 54: smiTest1 54: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 54: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 54: Test timeout computed to be: 1500 test 55 Start 55: smiTest2 55: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 55: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 55: Test timeout computed to be: 1500 test 56 Start 56: cxsmilesTest 56: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 56: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 56: Test timeout computed to be: 1500 test 57 Start 57: smaTest1 57: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 57: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 test 58 Start 58: smiTestCatch 58: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 58: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 1: [07:34:57] 1: 1: **** 1: Test Assert 1: Expression Failed: 1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp 1: Failed Expression: inchi == inchis[i] 1: **** 1: 1: [07:34:57] Invalid InChI prefix in generating InChI Key 1: [07:34:57] 1: 1: **** 1: Test Assert 1: Expression Failed: 1: Violation occurred on line 45 in file ./External/INCHI-API/test.cpp 1: Failed Expression: key2 == keys[i] 1: **** 1: 1: [07:34:57] 1: 1: **** 1: Test Assert 1: Expression Failed: 1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp 1: Failed Expression: inchi == inchis[i] 1: **** 1: 25: done 25: ------------------------------------- 25: Unit test for UFF butane scan. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing reading existing pickle file (v2). 34: -------------------------- 34: -------------------------- 34: C/C=C/C(C)Cl 34: [07:34:57] Conflicting single bond directions around double bond at index 2. 34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [07:34:57] Conflicting single bond directions around double bond at index 4. 34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [07:34:57] Conflicting single bond directions around double bond at index 15. 34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [07:34:57] Conflicting single bond directions around double bond at index 2. 34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [07:34:57] Conflicting single bond directions around double bond at index 1. 34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. 34: -------------------------------------------------- 17/223 Test #39: graphmolMemTest1 ....................... Passed 0.07 sec 18/223 Test #37: graphmolIterTest ....................... Passed 0.07 sec 36: [07:34:57] done 19/223 Test #36: graphmoltestPicklerGlobalSetting ....... Passed 0.08 sec 20/223 Test #41: molBundleTest .......................... Passed 0.07 sec 44: Randomness seeded to: 2401343911 44: [07:34:57] WARNING: not removing hydrogen atom without neighbors 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [07:34:57] Explicit valence for atom # 1 N, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 1 N, 6, is greater than permitted 44: [07:34:57] Explicit valence for atom # 1 N, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 1 N, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 2 O, 3, is greater than permitted 44: [07:34:57] Explicit valence for atom # 2 O, 3, is greater than permitted 44: [07:34:57] non-ring atom 2 marked aromatic 44: [07:34:57] non-ring atom 2 marked aromatic 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 1 2 3 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 1 2 3 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 44: [07:34:57] Explicit valence for atom # 1 O, 3, is greater than permitted 44: [07:34:57] Explicit valence for atom # 4 F, 2, is greater than permitted 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 44: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted 44: [07:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors 44: [07:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors 44: [07:34:57] WARNING: not removing hydrogen atom with wedged bond 44: [07:34:57] WARNING: not removing hydrogen atom without neighbors 44: [07:34:57] WARNING: not removing hydrogen atom without neighbors 46: Randomness seeded to: 2001951807 46: =============================================================================== 46: All tests passed (120 assertions in 6 test cases) 46: 50: Randomness seeded to: 3120086680 50: =============================================================================== 50: All tests passed (14 assertions in 4 test cases) 50: 21/223 Test #34: graphmoltestChirality .................. Passed 0.09 sec 22/223 Test #42: testSGroup ............................. Passed 0.07 sec 23/223 Test #43: test-valgrind .......................... Passed 0.05 sec 24/223 Test #46: graphmolSGroupCatch .................... Passed 0.04 sec test 59 Start 59: nontetrahedralCatch 59: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 test 60 Start 60: testDepictor 60: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor 60: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor 60: Test timeout computed to be: 1500 test 61 Start 61: depictorCatch 61: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch 61: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor 61: Test timeout computed to be: 1500 test 62 Start 62: pyDepictor 62: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" 62: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap 62: Test timeout computed to be: 1500 test 63 Start 63: testMrvToMol 63: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse 63: Test timeout computed to be: 1500 test 64 Start 64: fileParsersTest1 64: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 64: Test timeout computed to be: 1500 test 65 Start 65: testMolSupplier 65: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 65: Test timeout computed to be: 1500 test 66 Start 66: testGeneralFileReader 66: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 66: Test timeout computed to be: 1500 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing combining molecules using pickles. 35: Atoms: 35: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 35: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: Bonds: 35: 0 0->1 order: 1 conj?: 0 aromatic?: 0 35: 1 1->2 order: 1 conj?: 0 aromatic?: 0 35: 2 2->0 order: 1 conj?: 0 aromatic?: 0 35: 3 3->4 order: 1 conj?: 0 aromatic?: 0 35: 4 4->5 order: 1 conj?: 0 aromatic?: 0 35: 5 5->6 order: 1 conj?: 0 aromatic?: 0 35: 6 6->3 order: 1 conj?: 0 aromatic?: 0 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing Issue164: Roundtrip Pickle Failure. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing Issue219: Pickle Failure with Conformations. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing Issue220: Pickle problems with bond stereochemistry. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing query serialization. 35: [07:34:57] C=[$(C=O)] 35: [07:34:57] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] 44: [07:34:57] WARNING: not removing hydrogen atom without neighbors 44: [07:34:57] WARNING: not removing hydrogen atom without neighbors 44: [07:34:57] Unreasonable formal charge on hydrogen # 0. 44: [07:34:57] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() 44: [07:34:57] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: no atom 44: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: at 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: no owner 44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 44: Failed Expression: dp_mol 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: atom not associated with this molecule 44: Violation occurred on line 186 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: no atom 44: Violation occurred on line 385 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: at 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: no owner 44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 44: Failed Expression: dp_mol 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: atom not associated with this molecule 44: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: no atom 44: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: at 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: no owner 44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 44: Failed Expression: dp_mol 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: atom not associated with this molecule 44: Violation occurred on line 393 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: null atom passed in 44: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: atom_pin 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: cannot take ownership of an atom which already has an owner 44: Violation occurred on line 408 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: cannot take ownership of an bond which already has an owner 44: Violation occurred on line 434 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 44: **** 44: 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [07:34:57] WARNING: not removing hydrogen atom without neighbors 44: [07:34:57] Explicit valence for atom # 1 F greater than permitted 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: plain atoms have no Query 44: Violation occurred on line 610 in file ./Code/GraphMol/Atom.cpp 44: Failed Expression: 0 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: plain atoms have no Query 44: Violation occurred on line 615 in file ./Code/GraphMol/Atom.cpp 44: Failed Expression: 0 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: plain bonds have no Query 44: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp 44: Failed Expression: 0 44: **** 44: 44: [07:34:57] 44: 44: **** 44: Pre-condition Violation 44: plain bonds have no query 44: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp 44: Failed Expression: 0 44: **** 44: 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [07:34:57] Unusual charge on atom 0 number of radical electrons set to zero 44: [07:34:57] Unusual charge on atom 0 number of radical electrons set to zero 44: [07:34:57] Unusual charge on atom 0 number of radical electrons set to zero 44: [07:34:57] non-ring atom 0 marked aromatic 44: [07:34:57] non-ring atom 0 marked aromatic 44: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 9 C, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 3 N, 4, is greater than permitted 44: [07:34:57] Explicit valence for atom # 15 C, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 11 C, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 9 C, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 9 C, 5, is greater than permitted 44: [07:34:57] Explicit valence for atom # 9 C, 6, is greater than permitted 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 7 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 3 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 3 7 44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 3 7 25/223 Test #50: moliteratorTestsCatch .................. Passed 0.05 sec 55: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' 55: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 55: [07:34:57] SMILES Parse Error: syntax error while parsing: - 55: [07:34:57] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' 55: [07:34:57] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' 55: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' 55: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 55: [07:34:57] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' 55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' 55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' 55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' 55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' 55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' 55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' 55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' 26/223 Test #55: smiTest2 ............................... Passed 0.04 sec 51: Randomness seeded to: 3425740349 51: =============================================================================== 51: All tests passed (10 assertions in 1 test case) 51: 27/223 Test #51: queryTestsCatch ........................ Passed 0.05 sec 52: Randomness seeded to: 1569010506 52: =============================================================================== 52: All tests passed (6 assertions in 1 test case) 52: 28/223 Test #52: molbundleTestsCatch .................... Passed 0.05 sec 45: Randomness seeded to: 893550468 45: =============================================================================== 45: All tests passed (62 assertions in 6 test cases) 45: 29/223 Test #45: graphmolOrganometallicsCatch ........... Passed 0.06 sec 49: Randomness seeded to: 1172305161 49: =============================================================================== 49: All tests passed (137 assertions in 7 test cases) 49: 53: Randomness seeded to: 297128328 53: =============================================================================== 53: All tests passed (34 assertions in 1 test case) 53: 48: Randomness seeded to: 1002468320 48: [07:34:57] unable to set wavy bonds for double bonds: 3 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] WARNING: not removing hydrogen atom without neighbors 54: [07:34:57] Invalid chiral specification on atom 0 54: [07:34:57] Invalid chiral specification on atom 0 54: [07:34:57] Invalid chiral specification on atom 0 54: [07:34:57] Invalid chiral specification on atom 0 54: [07:34:57] Invalid chiral specification on atom 0 2: cyclosporine a 2: RDKit 2D 2: 2: 85 85 0 0 0 0 0 0 0 0999 V2000 2: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 3 2 1 1 2: 3 4 1 0 2: 4 5 2 0 2: 4 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 2 0 2: 8 10 1 0 2: 10 11 1 0 2: 11 12 1 0 2: 12 13 2 0 2: 12 14 1 0 2: 14 15 1 0 2: 15 16 1 0 2: 16 17 2 0 2: 16 18 1 0 2: 18 19 1 0 2: 19 20 1 0 2: 20 21 2 0 2: 20 22 1 0 2: 22 23 1 0 2: 23 24 1 0 2: 24 25 2 0 2: 24 26 1 0 2: 26 27 1 0 2: 27 28 1 0 2: 28 29 2 0 2: 28 30 1 0 2: 30 31 1 0 2: 31 32 1 0 2: 32 33 2 0 2: 32 34 1 0 2: 34 35 1 0 2: 35 36 1 0 2: 36 37 2 0 2: 36 38 1 0 2: 38 39 1 0 2: 39 40 1 0 2: 40 41 2 0 2: 40 42 1 0 2: 43 42 1 6 2: 43 44 1 0 2: 44 45 2 0 2: 44 46 1 0 2: 43 47 1 0 2: 47 48 1 0 2: 48 49 1 6 2: 48 50 1 0 2: 50 51 1 0 2: 51 52 2 0 2: 52 53 1 0 2: 47 54 1 1 2: 42 55 1 0 2: 39 56 1 6 2: 56 57 1 0 2: 56 58 1 0 2: 38 59 1 0 2: 35 60 1 6 2: 60 61 1 0 2: 61 62 1 0 2: 61 63 1 0 2: 34 64 1 0 2: 31 65 1 6 2: 65 66 1 0 2: 66 67 1 0 2: 66 68 1 0 2: 30 69 1 0 2: 27 70 1 6 2: 23 71 1 6 2: 19 72 1 6 2: 72 73 1 0 2: 73 74 1 0 2: 73 75 1 0 2: 18 76 1 0 2: 15 77 1 6 2: 77 78 1 0 2: 77 79 1 0 2: 11 80 1 6 2: 80 81 1 0 2: 81 82 1 0 2: 81 83 1 0 2: 10 84 1 0 2: 6 85 1 0 2: 46 3 1 0 2: M END 2: 2: single-double 2: RDKit 2D 2: 2: 17 16 0 0 0 0 0 0 0 0999 V2000 2: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 2 3 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 9 10 1 0 2: 10 11 2 3 2: 11 12 1 0 2: 12 13 2 3 2: 13 14 1 0 2: 14 15 2 3 2: 15 16 1 0 2: 16 17 1 0 2: M END 2: 2: cis-trans 2: RDKit 2D 2: 2: 10 9 0 0 0 0 0 0 0 0999 V2000 2: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 2 0 2: 3 4 1 0 2: 4 5 2 0 2: 5 6 1 0 2: 6 7 2 0 2: 7 8 1 0 2: 8 9 2 0 2: 9 10 1 0 2: M END 2: 2: admntn 2: RDKit 2D 2: 2: 10 12 0 0 0 0 0 0 0 0999 V2000 2: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 3 4 1 0 2: 4 5 1 0 2: 5 6 1 0 2: 6 7 1 0 2: 7 8 1 0 2: 8 9 1 0 2: 6 10 1 0 2: 8 1 1 0 2: 9 4 1 0 2: 10 2 1 0 2: M END 2: 2: github 4845 - nan coordinates but no crash 2: RDKit 2D 2: 2: 42 44 0 0 0 0 0 0 0 0999 V2000 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 2: 1 2 1 0 2: 2 3 1 0 2: 2 4 2 0 2: 4 5 1 0 2: 5 6 3 0 2: 6 7 1 0 2: 7 8 2 0 2: 8 9 1 0 2: 9 10 3 0 2: 10 11 1 0 2: 11 12 2 0 2: 12 13 1 0 2: 13 14 3 0 2: 14 15 1 0 2: 15 16 2 0 2: 16 17 1 0 2: 16 18 1 0 2: 12 19 1 0 2: 19 20 2 0 2: 20 21 1 0 2: 20 22 1 0 2: 19 23 1 0 2: 23 24 3 0 2: 24 25 1 0 2: 25 26 1 0 2: 26 27 2 0 2: 27 28 2 0 2: 26 29 1 0 2: 29 30 3 0 2: 8 31 1 0 2: 31 32 2 0 2: 32 33 1 0 2: 32 34 1 0 2: 31 35 1 0 2: 35 36 3 0 2: 36 37 1 0 2: 37 38 2 0 2: 37 39 1 0 2: 39 40 2 0 2: 40 41 1 0 2: 40 42 1 0 2: 39 4 1 0 2: 15 7 1 0 2: 30 11 1 0 2: M END 2: 33: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 26: 26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 47: Randomness seeded to: 1825795064 47: =============================================================================== 47: All tests passed (281 assertions in 10 test cases) 47: 58: Randomness seeded to: 1906733627 58: [07:34:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 58: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 58: [07:34:57] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' 58: [07:34:57] SMARTS Parse Error: unclosed ring for input: 'C1C' 58: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 58: [07:34:57] SMARTS Parse Error: syntax error while parsing: C)foo 58: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' 58: [07:34:57] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| 58: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 30/223 Test #47: graphmolAdjustQueryCatch ............... Passed 0.07 sec 31/223 Test #49: canonTestsCatch ........................ Passed 0.06 sec 32/223 Test #53: pickleTestsCatch ....................... Passed 0.05 sec test 67 Start 67: testMultithreadedMolSupplier 67: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 test 68 Start 68: testMolWriter 68: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 68: Test timeout computed to be: 1500 test 69 Start 69: testTplParser 69: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 69: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 test 70 Start 70: testMol2ToMol 70: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 70: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 test 71 Start 71: testSequence 71: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence 71: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 test 72 Start 72: testExtendedStereoParsing 72: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 72: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 72: Test timeout computed to be: 1500 test 73 Start 73: fileParsersCatchTest 73: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 73: Test timeout computed to be: 1500 test 74 Start 74: testPropertyLists 74: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 74: Test timeout computed to be: 1500 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing radical handling in pickles. 35: [07:34:57] done 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing sf.net issue 2788233. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing sf.net issue 3202580. 35: mass! 13.0034 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing sf.net issue 3316407. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing sf.net issue 3496759. 35: smi match: *C *C 35: smi match: **=* **=* 35: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O 35: smi match: *OS(=O)OC *OS(=O)OC 35: smi match: *S(=O)(=O)OC *S(=O)(=O)OC 35: smi match: O=COC=O O=COC=O 35: smi match: OO OO 35: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 35: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 35: smi match: nnnOC=O nnnOC=O 35: smi match: *=C=N *=C=N 35: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 35: smi match: SP(S)=S SP(S)=S 35: smi match: NP(N)(N)=O NP(N)(N)=O 35: smi match: cN=[N+]=[N-] cN=[N+]=[N-] 35: smi match: *CC=O *CC=O 35: smi match: NNC=O NNC=O 35: smi match: * * 35: smi match: C=P C=P 35: smi match: CC(=N)Cl CC(=N)Cl 35: smi match: N=O N=O 35: smi match: ** ** 35: smi match: N=C=N N=C=N 35: smi match: [C-]#[NH+] [C-]#[NH+] 35: smi match: O=CON(C=O)C=O O=CON(C=O)C=O 35: smi match: N#CC[OH] N#CC[OH] 35: smi match: N#CC=O N#CC=O 35: smi match: N#CS(=O)=O N#CS(=O)=O 35: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 35: smi match: N#CN=N N#CN=N 35: smi match: N=NCC=O N=NCC=O 35: smi match: CCCCCCC CCCCCCC 35: smi match: OCCOCCO OCCOCCO 35: smi match: SS SS 35: smi match: [SH] [SH] 35: smi match: *1CC1 *1CC1 35: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] 35: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] 35: smi match: NC(=S)N=N NC(=S)N=N 35: smi match: N#CS N#CS 35: smi match: cC[N+] cC[N+] 35: smi match: C*C=S C*C=S 35: smi match: N[CH2]C#N N[CH2]C#N 35: smi match: O=C1CCO1 O=C1CCO1 35: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] 35: smi match: O=C1CCN1 O=C1CCN1 35: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 35: smi match: C=CC=CC=CC=C C=CC=CC=CC=C 35: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 35: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 35: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 35: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 35: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 35: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 35: smi match: cN(=O)~O cN(=O)~O 35: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 35: smi match: N~NC=O N~NC=O 35: smi match: *=N~C *=N~C 35: smi match: CO*(=O)=O CO*(=O)=O 35: smi match: * * 35: smi match: * * 35: smi match: *C=C *C=C 35: smi match: N#CS N#CS 35: smi match: *C=S *C=S 35: smi match: *N *N 35: smi match: *C(=C)C=O *C(=C)C=O 35: smi match: *C#C *C#C 35: smi match: N#CCO N#CCO 35: smi match: O=N(=O)CCO O=N(=O)CCO 35: smi match: N=CS N=CS 35: smi match: O=CNC(O)C=O O=CNC(O)C=O 35: smi match: C=C(C=O)C=O C=C(C=O)C=O 35: smi match: N=CC=O N=CC=O 35: smi match: *C(C=O)C=O *C(C=O)C=O 35: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 35: smi match: O=CC=CC=O O=CC=CC=O 35: smi match: O=CN(O)C=O O=CN(O)C=O 35: smi match: O=CN(S)C=O O=CN(S)C=O 35: smi match: O=CNC=O O=CNC=O 35: smi match: O=CNN=O O=CNN=O 35: smi match: O=CNNC=O O=CNNC=O 35: smi match: O=CNOC=O O=CNOC=O 35: smi match: O=CS O=CS 35: smi match: O=CSC=S O=CSC=S 35: smi match: S=CS S=CS 35: smi match: C=O C=O 35: smi match: *C=N *C=N 35: smi match: CCCCCCC CCCCCCC 35: smi match: CN=O CN=O 35: smi match: CS(=O)(=O)O CS(=O)(=O)O 35: smi match: O=C1CCO1 O=C1CCO1 35: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 35: smi match: C=CCO C=CCO 35: smi match: C=CC=N C=CC=N 35: smi match: C=CC=O C=CC=O 35: smi match: C=CC(=O)C=C C=CC(=O)C=C 35: smi match: C=CC=S C=CC=S 35: smi match: C=CC(=S)S C=CC(=S)S 35: smi match: *C=C(*)C=C *C=C(*)C=C 35: smi match: C=CC=N C=CC=N 35: smi match: *N(*)C=C *N(*)C=C 35: smi match: C=CN(=O)=O C=CN(=O)=O 35: smi match: C=CN(O)=O C=CN(O)=O 35: smi match: C=CO C=CO 35: smi match: C=COC=O C=COC=O 35: smi match: C=CS C=CS 35: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 35: smi match: C=NCO C=NCO 35: smi match: C=NC=O C=NC=O 35: smi match: C=NN C=NN 35: smi match: C=NN=C C=NN=C 35: smi match: C=NO C=NO 35: smi match: C=NOC=O C=NOC=O 35: smi match: C=N=O C=N=O 35: smi match: N#CS N#CS 35: smi match: *CN=O *CN=O 35: smi match: NCN NCN 35: smi match: ON=CCN=O ON=CCN=O 35: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 35: smi match: N=C(N)S N=C(N)S 35: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 35: smi match: NC=S NC=S 35: smi match: NC(N)=S NC(N)=S 35: smi match: C=CN C=CN 35: smi match: NOC=O NOC=O 35: smi match: C1CN1 C1CN1 35: smi match: O=C1NNNN1 O=C1NNNN1 35: smi match: N=C(N)C(=N)N N=C(N)C(=N)N 35: smi match: N=C(N)O N=C(N)O 35: smi match: N=C(N)C(=N)S N=C(N)C(=N)S 35: smi match: *C=N *C=N 35: smi match: N=CC=O N=CC=O 35: smi match: N=CS N=CS 35: smi match: N=C=N N=C=N 35: smi match: N=C=O N=C=O 35: smi match: N=C=S N=C=S 35: smi match: NOC(=O)O NOC(=O)O 35: smi match: *C(O)=S *C(O)=S 35: smi match: C=CO C=CO 35: smi match: ON=CC=NO ON=CC=NO 35: smi match: *C[SH](=O)=O *C[SH](=O)=O 35: smi match: OS(=O)=O OS(=O)=O 35: smi match: N#CS N#CS 35: smi match: C=C(S)S C=C(S)S 35: smi match: N=C(N)S N=C(N)S 35: smi match: N=C(S)S N=C(S)S 35: smi match: NC(=S)S NC(=S)S 35: smi match: O=CNS O=CNS 35: smi match: S S 35: smi match: [SiH4] [SiH4] 35: smi match: NS NS 35: smi match: NCN NCN 35: smi match: cC(c)(O)O cC(c)(O)O 35: smi match: *C(c)O *C(c)O 35: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 35: smi match: cS(=O)(=O)O cS(=O)(=O)O 35: smi match: *c1ccccn1=O *c1ccccn1=O 35: smi match: *c1ccccn1 *c1ccccn1 35: smi match: *c1nccccn1 *c1nccccn1 35: smi match: C1COCOC1 C1COCOC1 35: smi match: C=S C=S 35: smi match: c=S c=S 35: smi match: S=CS S=CS 35: smi match: C=CN(=O)=O C=CN(=O)=O 35: smi match: C=CN(=O)O C=CN(=O)O 35: smi match: N=CC=O N=CC=O 35: smi match: C=CS C=CS 35: smi match: SC(S)(S)S SC(S)(S)S 35: smi match: OS(O)(O)O OS(O)(O)O 35: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O 35: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O 35: smi match: N#CS N#CS 35: smi match: C=NO C=NO 35: smi match: C=N[SH]=N C=N[SH]=N 35: smi match: O=C(S)S O=C(S)S 35: smi match: N=C(S)S N=C(S)S 35: smi match: N=C(=N)S N=C(=N)S 35: smi match: O=N=O O=N=O 35: smi match: O=NO O=NO 35: smi match: ONO ONO 35: smi match: C1SCS1 C1SCS1 35: smi match: N=C=S N=C=S 35: smi match: N=C=N N=C=N 35: smi match: C1N=N1 C1N=N1 35: smi match: *CS *CS 35: smi match: SC(S)=C(S)S SC(S)=C(S)S 35: smi match: N=CC=NO N=CC=NO 35: smi match: N#CCC#N N#CCC#N 35: smi match: CON=O CON=O 35: smi match: C=CN C=CN 35: smi match: C=N[SH](=O)=O C=N[SH](=O)=O 35: smi match: NN=O NN=O 35: smi match: NC(=O)S NC(=O)S 35: smi match: N#CS N#CS 35: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 35: smi match: c=N c=N 35: smi match: C1COCO1 C1COCO1 35: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 35: smi match: O=CC=O O=CC=O 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 48: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 48: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 48: [07:34:57] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 48: [07:34:57] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 48: [07:34:57] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored 48: [07:34:57] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored 48: [07:34:57] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 48: =============================================================================== 48: All tests passed (1845 assertions in 63 test cases) 48: 54: [07:34:57] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' 54: [07:34:57] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 33: [07:34:57] non-ring atom 0 marked aromatic 33: [07:34:57] non-ring atom 0 marked aromatic 33: [07:34:57] Conflicting single bond directions around double bond at index 17. 33: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. 33: starting ring finding 33: done 33: starting ring finding 33: done 33: starting ring finding 33: done 33: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C 33: starting sanitization 33: done 33: starting sanitization 58: [07:34:57] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' 59: Randomness seeded to: 69754176 59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [07:34:57] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 59: =============================================================================== 59: All tests passed (308 assertions in 9 test cases) 59: 65: [07:34:57] 65: ----------------------------------------- 65: [07:34:57] 65: 65: **** 65: Invariant Violation 65: bad prop value 65: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 65: Failed Expression: nSwaps < 2 65: **** 65: 66: [07:34:57] 66: ----------------------------------------- 66: [07:34:57] Finished: testDetermineFormat() 66: [07:34:57] ----------------------------------------- 66: 66: [07:34:57] 66: ----------------------------------------- 66: [07:34:57] Finished: testSdf() 66: [07:34:57] ----------------------------------------- 66: 66: [07:34:57] 66: ----------------------------------------- 66: [07:34:57] Finished: testSmi() 66: [07:34:57] ----------------------------------------- 66: 66: [07:34:57] 66: ----------------------------------------- 64: *************************************** 64: *************************************** 64: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [07:34:57] bond with order 0 found on line 7. This is not part of the MDL specification. 67: [07:34:57] 67: ----------------------------------------- 33/223 Test #2: testCoordGen ........................... Passed 0.21 sec 34/223 Test #48: chiralityTestsCatch .................... Passed 0.11 sec 35/223 Test #59: nontetrahedralCatch .................... Passed 0.07 sec test 75 Start 75: XYZFileParserCatchTest 75: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 test 76 Start 76: cdxmlParserCatchTest 76: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 76: Test timeout computed to be: 1500 test 77 Start 77: molfileStereoCatchTest 77: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest 77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 35: smi match: O=CNOC=O O=CNOC=O 35: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 35: smi match: ONO ONO 35: smi match: ON(~O)~O ON(~O)~O 35: smi match: OC1COC(O)C1 OC1COC(O)C1 35: smi match: OC1CCOC1O OC1CCOC1O 35: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 35: smi match: N=[N+]=N N=[N+]=N 35: smi match: N#CN N#CN 35: smi match: C=NN=C C=NN=C 35: smi match: *CCN(C)C *CCN(C)C 35: smi match: CNN CNN 35: smi match: *CC *CC 35: smi match: OCS OCS 35: smi match: C1NO1 C1NO1 35: smi match: COS(C)(=O)=O COS(C)(=O)=O 35: smi match: C1CO1 C1CO1 35: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 35: smi match: *C(*)=C *C(*)=C 35: smi match: N#[NH+] N#[NH+] 35: smi match: C#NO C#NO 35: smi match: OOO OOO 35: smi match: OO OO 35: smi match: O~Cl(~O)~O O~Cl(~O)~O 35: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O 35: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 35: smi match: *N *N 35: smi match: *P *P 35: smi match: *S *S 35: smi match: *C(*)(*)C=C *C(*)(*)C=C 35: smi match: *C(*)(*)C=C *C(*)(*)C=C 35: smi match: *C(*)C=C *C(*)C=C 35: smi match: *CC=C *CC=C 35: smi match: CN=C=O CN=C=O 35: smi match: CN=C=S CN=C=S 35: smi match: *C=O *C=O 35: smi match: N=N N=N 35: smi match: SS SS 35: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 35: smi match: CSC(C)=N CSC(C)=N 35: smi match: COC(C)=N COC(C)=N 35: smi match: C=C=C C=C=C 35: smi match: *C(=O)OC=O *C(=O)OC=O 35: smi match: C=CC#N C=CC#N 35: smi match: C=CC=O C=CC=O 35: smi match: CC=CC(C)=O CC=CC(C)=O 35: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 35: smi match: C#CC#N C#CC#N 35: smi match: C#CC=O C#CC=O 35: smi match: C#CC(=O)OCC C#CC(=O)OCC 35: smi match: C#CC=O C#CC=O 35: smi match: *C(=O)C#C *C(=O)C#C 35: smi match: C=CC=O C=CC=O 35: smi match: *C(*)(*)O *C(*)(*)O 35: smi match: COS(O)(=O)=O COS(O)(=O)=O 35: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] 35: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 35: smi match: *C(*)(*)C=O *C(*)(*)C=O 35: smi match: *C(*)(*)C=O *C(*)(*)C=O 35: smi match: *C(*)C=O *C(*)C=O 35: smi match: *CC=O *CC=O 35: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 35: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 35: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 35: smi match: *C[SH](=O)=O *C[SH](=O)=O 35: smi match: * * 44: [07:34:57] Explicit valence for atom # 1 O, 3, is greater than permitted 44: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 44: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 44: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 44: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 44: =============================================================================== 44: All tests passed (1630 assertions in 89 test cases) 44: 33: done 33: starting ring finding 33: done 33: starting ring finding 33: done 33: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 36/223 Test #69: testTplParser .......................... Passed 0.05 sec 71: Sequence: GREG 71: HELM: PEPTIDE1{G.R.E.G}$$$$ 71: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 71: PDB: 71: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 71: CONECT 1 2 71: CONECT 2 3 71: CONECT 3 4 4 5 71: CONECT 5 6 71: CONECT 6 7 9 71: CONECT 7 8 8 16 71: CONECT 9 10 71: CONECT 10 11 71: CONECT 11 12 71: CONECT 12 13 71: CONECT 13 14 14 15 71: CONECT 16 17 71: CONECT 17 18 20 71: CONECT 18 19 19 25 71: CONECT 20 21 71: CONECT 21 22 71: CONECT 22 23 23 24 71: CONECT 25 26 71: CONECT 26 27 71: CONECT 27 28 28 29 71: END 71: 71: Sequence: TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN 71: 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}$$$$ 71: 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 71: PDB: 71: ATOM 1 N THR A 1 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 2 CA THR A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 3 C THR A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 4 O THR A 1 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 5 CB THR A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 6 OG1 THR A 1 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 7 CG2 THR A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 8 N THR A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 9 CA THR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 10 C THR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 11 O THR A 2 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 12 CB THR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 13 OG1 THR A 2 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 14 CG2 THR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 15 N CYS A 3 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 16 CA CYS A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 17 C CYS A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 18 O CYS A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 19 CB CYS A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 20 SG CYS A 3 0.000 0.000 0.000 1.00 0.00 S 71: ATOM 21 N CYS A 4 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 22 CA CYS A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 23 C CYS A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 24 O CYS A 4 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 25 CB CYS A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 26 SG CYS A 4 0.000 0.000 0.000 1.00 0.00 S 71: ATOM 27 N PRO A 5 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 28 CA PRO A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 29 C PRO A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 30 O PRO A 5 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 31 CB PRO A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 32 CG PRO A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 33 CD PRO A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 34 N SER A 6 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 35 CA SER A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 36 C SER A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 37 O SER A 6 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 38 CB SER A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 39 OG SER A 6 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 40 N ILE A 7 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 41 CA ILE A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 42 C ILE A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 43 O ILE A 7 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 44 CB ILE A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 45 CG1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 46 CG2 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 47 CD1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 48 N VAL A 8 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 49 CA VAL A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 50 C VAL A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 51 O VAL A 8 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 52 CB VAL A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 53 CG1 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 54 CG2 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 55 N ALA A 9 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 56 CA ALA A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 57 C ALA A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 58 O ALA A 9 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 59 CB ALA A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 60 N ARG A 10 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 61 CA ARG A 10 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 62 C ARG A 10 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 63 O ARG A 10 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 64 CB ARG A 10 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 65 CG ARG A 10 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 66 CD ARG A 10 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 67 NE ARG A 10 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 68 CZ ARG A 10 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 69 NH1 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 70 NH2 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 71 N SER A 11 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 72 CA SER A 11 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 73 C SER A 11 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 74 O SER A 11 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 75 CB SER A 11 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 76 OG SER A 11 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 77 N ASN A 12 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 78 CA ASN A 12 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 79 C ASN A 12 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 80 O ASN A 12 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 81 CB ASN A 12 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 82 CG ASN A 12 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 83 OD1 ASN A 12 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 84 ND2 ASN A 12 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 85 N PHE A 13 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 86 CA PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 87 C PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 88 O PHE A 13 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 89 CB PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 90 CG PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 91 CD1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 92 CD2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 93 CE1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 94 CE2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 95 CZ PHE A 13 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 96 N ASN A 14 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 97 CA ASN A 14 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 98 C ASN A 14 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 99 O ASN A 14 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 100 CB ASN A 14 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 101 CG ASN A 14 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 102 OD1 ASN A 14 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 103 ND2 ASN A 14 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 104 N VAL A 15 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 105 CA VAL A 15 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 106 C VAL A 15 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 107 O VAL A 15 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 108 CB VAL A 15 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 109 CG1 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 110 CG2 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 111 N CYS A 16 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 112 CA CYS A 16 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 113 C CYS A 16 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 114 O CYS A 16 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 115 CB CYS A 16 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 116 SG CYS A 16 0.000 0.000 0.000 1.00 0.00 S 71: ATOM 117 N ARG A 17 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 118 CA ARG A 17 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 119 C ARG A 17 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 120 O ARG A 17 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 121 CB ARG A 17 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 122 CG ARG A 17 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 123 CD ARG A 17 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 124 NE ARG A 17 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 125 CZ ARG A 17 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 126 NH1 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 127 NH2 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 128 N LEU A 18 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 129 CA LEU A 18 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 130 C LEU A 18 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 131 O LEU A 18 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 132 CB LEU A 18 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 133 CG LEU A 18 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 134 CD1 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 135 CD2 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 136 N PRO A 19 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 137 CA PRO A 19 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 138 C PRO A 19 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 139 O PRO A 19 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 140 CB PRO A 19 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 141 CG PRO A 19 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 142 CD PRO A 19 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 143 N GLY A 20 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 144 CA GLY A 20 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 145 C GLY A 20 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 146 O GLY A 20 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 147 N THR A 21 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 148 CA THR A 21 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 149 C THR A 21 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 150 O THR A 21 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 151 CB THR A 21 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 152 OG1 THR A 21 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 153 CG2 THR A 21 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 154 N PRO A 22 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 155 CA PRO A 22 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 156 C PRO A 22 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 157 O PRO A 22 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 158 CB PRO A 22 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 159 CG PRO A 22 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 160 CD PRO A 22 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 161 N GLU A 23 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 162 CA GLU A 23 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 163 C GLU A 23 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 164 O GLU A 23 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 165 CB GLU A 23 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 166 CG GLU A 23 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 167 CD GLU A 23 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 168 OE1 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 169 OE2 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 170 N ALA A 24 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 171 CA ALA A 24 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 172 C ALA A 24 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 173 O ALA A 24 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 174 CB ALA A 24 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 175 N ILE A 25 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 176 CA ILE A 25 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 177 C ILE A 25 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 178 O ILE A 25 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 179 CB ILE A 25 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 180 CG1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 181 CG2 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 182 CD1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 183 N CYS A 26 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 184 CA CYS A 26 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 185 C CYS A 26 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 186 O CYS A 26 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 187 CB CYS A 26 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 188 SG CYS A 26 0.000 0.000 0.000 1.00 0.00 S 71: ATOM 189 N ALA A 27 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 190 CA ALA A 27 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 191 C ALA A 27 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 192 O ALA A 27 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 193 CB ALA A 27 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 194 N THR A 28 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 195 CA THR A 28 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 196 C THR A 28 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 197 O THR A 28 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 198 CB THR A 28 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 199 OG1 THR A 28 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 200 CG2 THR A 28 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 201 N TYR A 29 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 202 CA TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 203 C TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 204 O TYR A 29 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 205 CB TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 206 CG TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 207 CD1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 208 CD2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 209 CE1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 210 CE2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 211 CZ TYR A 29 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 212 OH TYR A 29 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 213 N THR A 30 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 214 CA THR A 30 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 215 C THR A 30 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 216 O THR A 30 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 217 CB THR A 30 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 218 OG1 THR A 30 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 219 CG2 THR A 30 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 220 N GLY A 31 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 221 CA GLY A 31 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 222 C GLY A 31 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 223 O GLY A 31 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 224 N CYS A 32 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 225 CA CYS A 32 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 226 C CYS A 32 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 227 O CYS A 32 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 228 CB CYS A 32 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 229 SG CYS A 32 0.000 0.000 0.000 1.00 0.00 S 71: ATOM 230 N ILE A 33 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 231 CA ILE A 33 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 232 C ILE A 33 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 233 O ILE A 33 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 234 CB ILE A 33 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 235 CG1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 236 CG2 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 237 CD1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 238 N ILE A 34 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 239 CA ILE A 34 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 240 C ILE A 34 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 241 O ILE A 34 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 242 CB ILE A 34 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 243 CG1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 244 CG2 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 245 CD1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 246 N ILE A 35 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 247 CA ILE A 35 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 248 C ILE A 35 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 249 O ILE A 35 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 250 CB ILE A 35 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 251 CG1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 252 CG2 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 253 CD1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 254 N PRO A 36 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 255 CA PRO A 36 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 256 C PRO A 36 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 257 O PRO A 36 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 258 CB PRO A 36 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 259 CG PRO A 36 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 260 CD PRO A 36 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 261 N GLY A 37 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 262 CA GLY A 37 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 263 C GLY A 37 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 264 O GLY A 37 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 265 N ALA A 38 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 266 CA ALA A 38 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 267 C ALA A 38 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 268 O ALA A 38 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 269 CB ALA A 38 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 270 N THR A 39 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 271 CA THR A 39 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 272 C THR A 39 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 273 O THR A 39 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 274 CB THR A 39 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 275 OG1 THR A 39 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 276 CG2 THR A 39 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 277 N CYS A 40 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 278 CA CYS A 40 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 279 C CYS A 40 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 280 O CYS A 40 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 281 CB CYS A 40 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 282 SG CYS A 40 0.000 0.000 0.000 1.00 0.00 S 71: ATOM 283 N PRO A 41 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 284 CA PRO A 41 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 285 C PRO A 41 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 286 O PRO A 41 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 287 CB PRO A 41 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 288 CG PRO A 41 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 289 CD PRO A 41 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 290 N GLY A 42 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 291 CA GLY A 42 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 292 C GLY A 42 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 293 O GLY A 42 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 294 N ASP A 43 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 295 CA ASP A 43 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 296 C ASP A 43 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 297 O ASP A 43 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 298 CB ASP A 43 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 299 CG ASP A 43 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 300 OD1 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 301 OD2 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 302 N TYR A 44 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 303 CA TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 304 C TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 305 O TYR A 44 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 306 CB TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 307 CG TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 308 CD1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 309 CD2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 310 CE1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 311 CE2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 312 CZ TYR A 44 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 313 OH TYR A 44 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 314 N ALA A 45 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 315 CA ALA A 45 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 316 C ALA A 45 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 317 O ALA A 45 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 318 CB ALA A 45 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 319 N ASN A 46 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 320 CA ASN A 46 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 321 C ASN A 46 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 322 O ASN A 46 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 323 CB ASN A 46 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 324 CG ASN A 46 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 325 OD1 ASN A 46 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 326 ND2 ASN A 46 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 327 OXT ASN A 46 0.000 0.000 0.000 1.00 0.00 O 71: CONECT 1 2 71: CONECT 2 3 5 71: CONECT 3 4 4 8 71: CONECT 5 6 7 71: CONECT 8 9 71: CONECT 9 10 12 71: CONECT 10 11 11 15 71: CONECT 12 13 14 71: CONECT 15 16 71: CONECT 16 17 19 71: CONECT 17 18 18 21 71: CONECT 19 20 71: CONECT 21 22 71: CONECT 22 23 25 71: CONECT 23 24 24 27 71: CONECT 25 26 71: CONECT 27 28 33 71: CONECT 28 29 31 71: CONECT 29 30 30 34 71: CONECT 31 32 71: CONECT 32 33 71: CONECT 34 35 71: CONECT 35 36 38 71: CONECT 36 37 37 40 71: CONECT 38 39 71: CONECT 40 41 71: CONECT 41 42 44 71: CONECT 42 43 43 48 71: CONECT 44 45 46 71: CONECT 46 47 71: CONECT 48 49 71: CONECT 49 50 52 71: CONECT 50 51 51 55 71: CONECT 52 53 54 71: CONECT 55 56 71: CONECT 56 57 59 71: CONECT 57 58 58 60 71: CONECT 60 61 71: CONECT 61 62 64 71: CONECT 62 63 63 71 71: CONECT 64 65 71: CONECT 65 66 71: CONECT 66 67 71: CONECT 67 68 71: CONECT 68 69 69 70 71: CONECT 71 72 71: CONECT 72 73 75 71: CONECT 73 74 74 77 71: CONECT 75 76 71: CONECT 77 78 71: CONECT 78 79 81 71: CONECT 79 80 80 85 71: CONECT 81 82 71: CONECT 82 83 83 84 71: CONECT 85 86 71: CONECT 86 87 89 71: CONECT 87 88 88 96 71: CONECT 89 90 71: CONECT 90 91 91 92 71: CONECT 91 93 71: CONECT 92 94 94 71: CONECT 93 95 95 71: CONECT 94 95 71: CONECT 96 97 71: CONECT 97 98 100 71: CONECT 98 99 99 104 71: CONECT 100 101 71: CONECT 101 102 102 103 71: CONECT 104 105 71: CONECT 105 106 108 71: CONECT 106 107 107 111 71: CONECT 108 109 110 71: CONECT 111 112 71: CONECT 112 113 115 71: CONECT 113 114 114 117 71: CONECT 115 116 71: CONECT 117 118 71: CONECT 118 119 121 71: CONECT 119 120 120 128 71: CONECT 121 122 71: CONECT 122 123 71: CONECT 123 124 71: CONECT 124 125 71: CONECT 125 126 126 127 71: CONECT 128 129 71: CONECT 129 130 132 71: CONECT 130 131 131 136 71: CONECT 132 133 71: CONECT 133 134 135 71: CONECT 136 137 142 71: CONECT 137 138 140 71: CONECT 138 139 139 143 71: CONECT 140 141 71: CONECT 141 142 71: CONECT 143 144 71: CONECT 144 145 71: CONECT 145 146 146 147 71: CONECT 147 148 71: CONECT 148 149 151 71: CONECT 149 150 150 154 71: CONECT 151 152 153 71: CONECT 154 155 160 71: CONECT 155 156 158 71: CONECT 156 157 157 161 71: CONECT 158 159 71: CONECT 159 160 71: CONECT 161 162 71: CONECT 162 163 165 71: CONECT 163 164 164 170 71: CONECT 165 166 71: CONECT 166 167 71: CONECT 167 168 168 169 71: CONECT 170 171 71: CONECT 171 172 174 71: CONECT 172 173 173 175 71: CONECT 175 176 71: CONECT 176 177 179 71: CONECT 177 178 178 183 71: CONECT 179 180 181 71: CONECT 181 182 71: CONECT 183 184 71: CONECT 184 185 187 71: CONECT 185 186 186 189 71: CONECT 187 188 71: CONECT 189 190 71: CONECT 190 191 193 71: CONECT 191 192 192 194 71: CONECT 194 195 71: CONECT 195 196 198 71: CONECT 196 197 197 201 71: CONECT 198 199 200 71: CONECT 201 202 71: CONECT 202 203 205 71: CONECT 203 204 204 213 71: CONECT 205 206 71: CONECT 206 207 207 208 71: CONECT 207 209 71: CONECT 208 210 210 71: CONECT 209 211 211 71: CONECT 210 211 71: CONECT 211 212 71: CONECT 213 214 71: CONECT 214 215 217 71: CONECT 215 216 216 220 71: CONECT 217 218 219 71: CONECT 220 221 71: CONECT 221 222 71: CONECT 222 223 223 224 71: CONECT 224 225 71: CONECT 225 226 228 71: CONECT 226 227 227 230 71: CONECT 228 229 71: CONECT 230 231 71: CONECT 231 232 234 71: CONECT 232 233 233 238 71: CONECT 234 235 236 71: CONECT 236 237 71: CONECT 238 239 71: CONECT 239 240 242 71: CONECT 240 241 241 246 71: CONECT 242 243 244 71: CONECT 244 245 71: CONECT 246 247 71: CONECT 247 248 250 71: CONECT 248 249 249 254 71: CONECT 250 251 252 71: CONECT 252 253 71: CONECT 254 255 260 71: CONECT 255 256 258 71: CONECT 256 257 257 261 71: CONECT 258 259 71: CONECT 259 260 71: CONECT 261 262 71: CONECT 262 263 71: CONECT 263 264 264 265 71: CONECT 265 266 71: CONECT 266 267 269 71: CONECT 267 268 268 270 71: CONECT 270 271 71: CONECT 271 272 274 71: CONECT 272 273 273 277 71: CONECT 274 275 276 71: CONECT 277 278 71: CONECT 278 279 281 71: CONECT 279 280 280 283 71: CONECT 281 282 71: CONECT 283 284 289 71: CONECT 284 285 287 71: CONECT 285 286 286 290 71: CONECT 287 288 71: CONECT 288 289 71: CONECT 290 291 71: CONECT 291 292 71: CONECT 292 293 293 294 71: CONECT 294 295 71: CONECT 295 296 298 71: CONECT 296 297 297 302 71: CONECT 298 299 71: CONECT 299 300 300 301 71: CONECT 302 303 71: CONECT 303 304 306 71: CONECT 304 305 305 314 71: CONECT 306 307 71: CONECT 307 308 308 309 71: CONECT 308 310 71: CONECT 309 311 311 71: CONECT 310 312 312 71: CONECT 311 312 71: CONECT 312 313 71: CONECT 314 315 71: CONECT 315 316 318 71: CONECT 316 317 317 319 71: CONECT 319 320 71: CONECT 320 321 323 71: CONECT 321 322 322 327 71: CONECT 323 324 71: CONECT 324 325 325 326 71: END 71: 71: Sequence: GREG 71: HELM: PEPTIDE1{G.R.E.G}$$$$ 71: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O 71: PDB: 71: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 71: CONECT 1 2 71: CONECT 2 3 71: CONECT 3 4 4 5 71: CONECT 5 6 71: CONECT 6 7 9 71: CONECT 7 8 8 16 71: CONECT 9 10 71: CONECT 10 11 71: CONECT 11 12 71: CONECT 12 13 71: CONECT 13 14 14 15 71: CONECT 16 17 71: CONECT 17 18 20 71: CONECT 18 19 19 25 71: CONECT 20 21 71: CONECT 21 22 71: CONECT 22 23 23 24 71: CONECT 25 26 71: CONECT 26 27 71: CONECT 27 28 28 29 71: END 71: 71: Sequence: CYIQNCPLG 71: HELM: PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$ 71: 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 71: PDB: 71: ATOM 1 N CYS A 1 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 2 CA CYS A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 3 C CYS A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 4 O CYS A 1 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 5 CB CYS A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 6 SG CYS A 1 0.000 0.000 0.000 1.00 0.00 S 71: ATOM 7 N TYR A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 8 CA TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 9 C TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 10 O TYR A 2 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 11 CB TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 12 CG TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 13 CD1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 14 CD2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 15 CE1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 16 CE2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 17 CZ TYR A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 18 OH TYR A 2 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 19 N ILE A 3 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 20 CA ILE A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 21 C ILE A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 22 O ILE A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 23 CB ILE A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 24 CG1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 25 CG2 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 26 CD1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 27 N GLN A 4 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 28 CA GLN A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 29 C GLN A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 30 O GLN A 4 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 31 CB GLN A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O 37/223 Test #72: testExtendedStereoParsing .............. Passed 0.04 sec test 78 Start 78: connectTheDotsTest 78: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 78: Test timeout computed to be: 1500 test 79 Start 79: testSubstructMatch 79: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct 79: Test timeout computed to be: 1500 35: smi match: *1CC1 *1CC1 35: smi match: O=COC=O O=COC=O 35: smi match: N=C=O N=C=O 35: smi match: N=C=S N=C=S 35: smi match: O~O O~O 35: smi match: N~[SiH4] N~[SiH4] 35: smi match: *P *P 35: smi match: C=N=N C=N=N 35: smi match: *N#[NH+] *N#[NH+] 35: smi match: *S* *S* 35: smi match: ** ** 35: smi match: *CC* *CC* 35: smi match: *O[SiH3] *O[SiH3] 35: smi match: *OS(*)~O *OS(*)~O 35: smi match: N~N~O N~N~O 35: smi match: *N(~O)(~O)~O *N(~O)(~O)~O 35: smi match: *[N+](=C)[O-] *[N+](=C)[O-] 35: smi match: * * 35: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 35: smi match: *OCC#N *OCC#N 35: smi match: **C=C **C=C 35: smi match: C=C[O-] C=C[O-] 35: smi match: C=CO C=CO 35: smi match: * * 35: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 35: smi match: O=COn1ccnc1 O=COn1ccnc1 35: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 35: smi match: CC(C)(C)S CC(C)(C)S 35: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C 35: smi match: [CH]=O [CH]=O 35: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 35: smi match: SS SS 35: smi match: [SH] [SH] 35: smi match: *C* *C* 35: smi match: * * 35: smi match: C[nH3+] C[nH3+] 35: smi match: cC(=N)[NH2] cC(=N)[NH2] 35: smi match: O=CN[OH] O=CN[OH] 35: smi match: NN NN 35: smi match: * * 35: smi match: *OP(=O)O* *OP(=O)O* 35: smi match: * * 35: smi match: * * 35: smi match: * * 35: smi match: *N=C(*)* *N=C(*)* 35: smi match: *C(*)(*)C=O *C(*)(*)C=O 35: smi match: CSC=O CSC=O 35: smi match: * * 35: smi match: O=CCl O=CCl 35: smi match: *** *** 35: smi match: *C=O *C=O 35: smi match: C[OH] C[OH] 35: smi match: C[OH] C[OH] 35: smi match: C[OH] C[OH] 35: smi match: C[OH] C[OH] 35: smi match: C[CH]=O C[CH]=O 35: smi match: *=* *=* 35: smi match: *C *C 35: smi match: C#C C#C 35: smi match: *[CH]C=C *[CH]C=C 38/223 Test #44: graphmolTestsCatch ..................... Passed 0.15 sec 33: [07:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors 33: ------------------------------- 33: [07:34:57] Explicit valence for atom # 0 N, 4, is greater than permitted 33: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 33: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 33: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 33: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 15: ......... 15: ---------------------------------------------------------------------- 15: Ran 9 tests in 0.014s 15: 15: OK 14: ......... 14: ---------------------------------------------------------------------- 14: Ran 9 tests in 0.008s 14: 14: OK 71: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 38 C ASN A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 39 O ASN A 5 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 40 CB ASN A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 41 CG ASN A 5 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 42 OD1 ASN A 5 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 43 ND2 ASN A 5 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 44 N CYS A 6 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 45 CA CYS A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 46 C CYS A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 47 O CYS A 6 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 48 CB CYS A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 49 SG CYS A 6 0.000 0.000 0.000 1.00 0.00 S 71: ATOM 50 N PRO A 7 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 51 CA PRO A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 52 C PRO A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 53 O PRO A 7 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 54 CB PRO A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 55 CG PRO A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 56 CD PRO A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 57 N LEU A 8 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 58 CA LEU A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 59 C LEU A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 60 O LEU A 8 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 61 CB LEU A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 62 CG LEU A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 63 CD1 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 64 CD2 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 65 N GLY A 9 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 66 CA GLY A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 67 C GLY A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 68 O GLY A 9 0.000 0.000 0.000 1.00 0.00 O 71: HETATM 69 N NH2 A 10 0.000 0.000 0.000 1.00 0.00 N 71: CONECT 1 2 71: CONECT 2 3 5 71: CONECT 3 4 4 7 71: CONECT 5 6 71: CONECT 6 49 71: CONECT 7 8 71: CONECT 8 9 11 71: CONECT 9 10 10 19 71: CONECT 11 12 71: CONECT 12 13 13 14 71: CONECT 13 15 71: CONECT 14 16 16 71: CONECT 15 17 17 71: CONECT 16 17 71: CONECT 17 18 71: CONECT 19 20 71: CONECT 20 21 23 71: CONECT 21 22 22 27 71: CONECT 23 24 25 71: CONECT 25 26 71: CONECT 27 28 71: CONECT 28 29 31 71: CONECT 29 30 30 36 71: CONECT 31 32 71: CONECT 32 33 71: CONECT 33 34 34 35 71: CONECT 36 37 71: CONECT 37 38 40 71: CONECT 38 39 39 44 71: CONECT 40 41 71: CONECT 41 42 42 43 71: CONECT 44 45 71: CONECT 45 46 48 71: CONECT 46 47 47 50 71: CONECT 48 49 71: CONECT 50 51 56 71: CONECT 51 52 54 71: CONECT 52 53 53 57 71: CONECT 54 55 71: CONECT 55 56 71: CONECT 57 58 71: CONECT 58 59 61 71: CONECT 59 60 60 65 71: CONECT 61 62 71: CONECT 62 63 64 71: CONECT 65 66 71: CONECT 66 67 71: CONECT 67 68 68 69 71: END 71: 71: Sequence: LfPVXLfPVX 71: HELM: PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$ 71: 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 71: PDB: 71: ATOM 1 N LEU A 1 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 2 CA LEU A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 3 C LEU A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 4 O LEU A 1 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 5 CB LEU A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 6 CG LEU A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 7 CD1 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 8 CD2 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 9 N DPN A 2 0.000 0.000 0.000 1.00 0.00 N 71: HETATM 10 CA DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 11 C DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 12 O DPN A 2 0.000 0.000 0.000 1.00 0.00 O 71: HETATM 13 CB DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 14 CG DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 15 CD1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 16 CD2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 17 CE1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 18 CE2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 19 CZ DPN A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 20 N PRO A 3 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 21 CA PRO A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 22 C PRO A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 23 O PRO A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 24 CB PRO A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 25 CG PRO A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 26 CD PRO A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 27 N VAL A 4 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 28 CA VAL A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 29 C VAL A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 30 O VAL A 4 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 31 CB VAL A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 32 CG1 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 33 CG2 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 34 N ORN A 5 0.000 0.000 0.000 1.00 0.00 N 71: HETATM 35 CA ORN A 5 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 36 C ORN A 5 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 37 O ORN A 5 0.000 0.000 0.000 1.00 0.00 O 71: HETATM 38 CB ORN A 5 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 39 CG ORN A 5 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 40 CD ORN A 5 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 41 NE ORN A 5 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 42 N LEU A 6 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 43 CA LEU A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 44 C LEU A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 45 O LEU A 6 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 46 CB LEU A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 47 CG LEU A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N 71: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O 71: HETATM 54 CB DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 55 CG DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 56 CD1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 57 CD2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 58 CE1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 59 CE2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 60 CZ DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 61 N PRO A 8 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 62 CA PRO A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 63 C PRO A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 64 O PRO A 8 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 65 CB PRO A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 66 CG PRO A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 67 CD PRO A 8 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 68 N VAL A 9 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 69 CA VAL A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 70 C VAL A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 71 O VAL A 9 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 72 CB VAL A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 73 CG1 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 74 CG2 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 75 N ORN A 10 0.000 0.000 0.000 1.00 0.00 N 71: HETATM 76 CA ORN A 10 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 77 C ORN A 10 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 78 O ORN A 10 0.000 0.000 0.000 1.00 0.00 O 71: HETATM 79 CB ORN A 10 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 80 CG ORN A 10 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 81 CD ORN A 10 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 82 NE ORN A 10 0.000 0.000 0.000 1.00 0.00 N 71: CONECT 1 2 77 71: CONECT 2 3 5 71: CONECT 3 4 4 9 71: CONECT 5 6 71: CONECT 6 7 8 71: CONECT 9 10 71: CONECT 10 11 13 71: CONECT 11 12 12 20 71: CONECT 13 14 71: CONECT 14 15 15 16 71: CONECT 15 17 71: CONECT 16 18 18 71: CONECT 17 19 19 71: CONECT 18 19 71: CONECT 20 21 26 71: CONECT 21 22 24 71: CONECT 22 23 23 27 71: CONECT 24 25 71: CONECT 25 26 71: CONECT 27 28 71: CONECT 28 29 31 71: CONECT 29 30 30 34 71: CONECT 31 32 33 71: CONECT 34 35 71: CONECT 35 36 38 71: CONECT 36 37 37 42 71: CONECT 38 39 71: CONECT 39 40 71: CONECT 40 41 71: CONECT 42 43 71: CONECT 43 44 46 71: CONECT 44 45 45 50 71: CONECT 46 47 71: CONECT 47 48 49 71: CONECT 50 51 71: CONECT 51 52 54 71: CONECT 52 53 53 61 71: CONECT 54 55 71: CONECT 55 56 56 57 71: CONECT 56 58 71: CONECT 57 59 59 71: CONECT 58 60 60 71: CONECT 59 60 71: CONECT 61 62 67 71: CONECT 62 63 65 71: CONECT 63 64 64 68 71: CONECT 65 66 71: CONECT 66 67 71: CONECT 68 69 71: CONECT 69 70 72 71: CONECT 70 71 71 75 71: CONECT 72 73 74 71: CONECT 75 76 71: CONECT 76 77 79 71: CONECT 77 78 78 71: CONECT 79 80 71: CONECT 80 81 71: CONECT 81 82 71: END 71: 71: Sequence: GREG 71: HELM: PEPTIDE1{G.R.E.G}$$$$ 71: Smiles: N=C(N)NCCCC(NC(=O)CN)C(=O)NC(CCC(=O)O)C(=O)NCC(=O)O 71: PDB: 71: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 23 OD1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 24 OD2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 71: CONECT 1 2 71: CONECT 2 3 71: CONECT 3 4 4 5 71: CONECT 5 6 71: CONECT 6 7 9 71: CONECT 7 8 8 16 71: CONECT 9 10 71: CONECT 10 11 71: CONECT 11 12 71: CONECT 12 13 71: CONECT 13 14 14 15 71: CONECT 16 17 71: CONECT 17 18 20 71: CONECT 18 19 19 25 71: CONECT 20 21 71: CONECT 21 22 71: CONECT 22 23 23 24 71: CONECT 25 26 71: CONECT 26 27 71: CONECT 27 28 28 29 71: END 71: 64: [07:34:57] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 64: [07:34:57] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 64: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 64: generating smiles 64: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 64: converting back 64: check isomorphism 74: Randomness seeded to: 3484029761 74: =============================================================================== 74: All tests passed (95 assertions in 4 test cases) 74: 63: Using new chirality perception 63: Test 63: 63: NewChiralTest.sdf 63: 63: Test 63: 63: NewChiralTest.sdf 63: 63: Test 63: 63: NewChiralTestNoChiral.sdf 63: 63: Test 63: 63: NewChiralTestNoChiral.sdf 63: 63: Test 63: 63: NewChiralTestAllChiral.sdf 63: 63: Test 63: 63: NewChiralTestAllChiral.sdf 63: 63: Test 63: 63: ProblemShort.mol 63: 63: [07:34:57] For a MultipleSgroup expansion, the matching orphaned bond was not found 63: The multiple sgroup will be ignored 23: ..... 23: ---------------------------------------------------------------------- 23: Ran 5 tests in 0.002s 23: 23: OK 23: Testing Alignment Wrapper code: 73: Randomness seeded to: 781856005 73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 73: [07:34:57] Could not infer missing lvIdx on malformed SAP line for SGroup 1 73: [07:34:57] SGroup 1 is invalid and will be ignored 73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 73: [07:34:57] Could not infer missing lvIdx on malformed SAP line for SGroup 1 73: [07:34:57] SGroup 1 is invalid and will be ignored 73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 73: [07:34:57] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 73: [07:34:57] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 73: [07:34:57] Could not infer missing lvIdx on malformed SAP line for SGroup 1 73: [07:34:57] SGroup 1 is invalid and will be ignored 73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 73: [07:34:57] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 73: [07:34:57] Could not infer missing lvIdx on malformed SAP line for SGroup 1 73: [07:34:57] SGroup 1 is invalid and will be ignored 73: [07:34:57] SGroup 3 referenced on line 40 not found. 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: no bonds 73: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp 73: Failed Expression: !d_bonds.empty() 73: **** 73: 73: [07:34:57] SGroup 3 referenced on line 40 not found. 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: no bonds 73: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp 73: Failed Expression: !d_bonds.empty() 73: **** 73: 73: [07:34:57] no bonds 73: [07:34:57] SGroup 1 is invalid and will be ignored 73: [07:34:57] SGroup line too short: 'M SBV 1 6' on line 42 73: [07:34:57] SGroup 1 is invalid and will be ignored 73: [07:34:57] SGroup line too short: 'M SBL 2 3 9 10' on line 46 73: [07:34:57] SGroup 2 is invalid and will be ignored 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [07:34:57] bookmark not found 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bond is not part of the SubstanceGroup 73: Violation occurred on line 158 in file ./Code/GraphMol/SubstanceGroup.cpp 73: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 73: **** 73: 73: [07:34:57] bond is not part of the SubstanceGroup 73: [07:34:57] SGroup 2 is invalid and will be ignored 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [07:34:57] bookmark not found 73: [07:34:57] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. 73: [07:34:57] SGroup 2 is invalid and will be ignored 73: [07:34:57] WARNING: final character of V3000 array is not ')' 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [07:34:57] WARNING: final character of V3000 array is not ')' 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [07:34:57] bookmark not found 73: [07:34:57] SGroup 1 is invalid and will be ignored 73: [07:34:57] WARNING: final character of V3000 array is not ')' 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [07:34:57] WARNING: final character of V3000 array is not ')' 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [07:34:57] bookmark not found 73: [07:34:57] SGroup 1 is invalid and will be ignored 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [07:34:57] bookmark not found 73: [07:34:57] SGroup 2 is invalid and will be ignored 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [07:34:57] bookmark not found 73: [07:34:57] SGroup 2 is invalid and will be ignored 73: [07:34:57] Explicit valence for atom # 2 O, 3, is greater than permitted 73: [07:34:57] Explicit valence for atom # 1 O, 3, is greater than permitted 73: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted 73: [07:34:57] sanitize [07:34:57] UNK: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 3: .... 3: ---------------------------------------------------------------------- 3: Ran 4 tests in 0.029s 3: 3: OK 13: ...... 13: ---------------------------------------------------------------------- 13: Ran 6 tests in 0.002s 13: 13: OK 39/223 Test #70: testMol2ToMol .......................... Passed 0.09 sec 40/223 Test #71: testSequence ........................... Passed 0.08 sec 41/223 Test #74: testPropertyLists ...................... Passed 0.07 sec test 80 Start 80: substructTestCatch 80: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct 80: Test timeout computed to be: 1500 test 81 Start 81: testGenericGroups 81: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups 81: Test timeout computed to be: 1500 test 82 Start 82: testReaction 82: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 82: Test timeout computed to be: 1500 test 83 Start 83: testReactionFingerprints 83: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 83: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 83: Test timeout computed to be: 1500 35: smi match: cCC(=O)[OH] cCC(=O)[OH] 35: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 35: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] 35: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 35: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 35: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O 35: smi match: *N(*)C*=O *N(*)C*=O 35: smi match: O=*C[OH] O=*C[OH] 35: smi match: *=C*=O *=C*=O 35: smi match: *=CC#N *=CC#N 35: smi match: *C[OH] *C[OH] 35: smi match: ** ** 35: smi match: *C[OH] *C[OH] 35: smi match: *C(*)=O *C(*)=O 35: smi match: * * 35: smi match: *CC(=O)[OH] *CC(=O)[OH] 35: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 35: smi match: *c *c 35: smi match: CN(C)c CN(C)c 35: smi match: c c 35: smi match: *c *c 35: smi match: *c *c 35: smi match: **:*cF **:*cF 35: smi match: cB([OH])[OH] cB([OH])[OH] 35: smi match: N~N~N N~N~N 35: smi match: *N=N* *N=N* 35: smi match: *CC[OH] *CC[OH] 35: smi match: *CC[OH] *CC[OH] 35: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] 35: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 35: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 35: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] 35: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O 35: smi match: *OC(*)=O *OC(*)=O 35: smi match: *C(=O)[OH] *C(=O)[OH] 35: smi match: O=C[OH] O=C[OH] 35: smi match: *OC(=O)O* *OC(=O)O* 35: smi match: * * 35: smi match: *OC(=O)Cl *OC(=O)Cl 35: smi match: *C#N *C#N 35: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 35: smi match: SS SS 35: smi match: * * 35: smi match: *=* *=* 35: smi match: *=* *=* 35: smi match: *=* *=* 35: smi match: *=* *=* 35: smi match: C1CO1 C1CO1 35: smi match: *OC(*)=O *OC(*)=O 35: smi match: * * 35: smi match: *O*[OH] *O*[OH] 35: smi match: COC(C)(C)O COC(C)(C)O 35: smi match: *[OH] *[OH] 35: smi match: ** ** 35: smi match: C=N[NH2] C=N[NH2] 35: smi match: C=NC=O C=NC=O 35: smi match: * * 35: smi match: C#NC C#NC 35: smi match: CN=C=O CN=C=O 35: smi match: CN=C=S CN=C=S 35: smi match: *OC(*)(*)O* *OC(*)(*)O* 35: smi match: *C(*)=O *C(*)=O 35: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 35: smi match: *~*=O *~*=O 35: smi match: *~*=O *~*=O 35: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] 35: smi match: * * 35: smi match: *C#N *C#N 35: smi match: *N(=O)~O *N(=O)~O 35: smi match: N N 35: smi match: OC(=O)C(O)=O OC(=O)C(O)=O 35: smi match: C=NO C=NO 35: smi match: O~O O~O 35: smi match: c[OH] c[OH] 35: smi match: O=P(~[OH])~O O=P(~[OH])~O 35: smi match: CO~P(=O)~O CO~P(=O)~O 35: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O 35: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 35: smi match: O=P(~O)~O O=P(~O)~O 35: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O 35: smi match: C[NH2] C[NH2] 35: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 35: smi match: * * 35: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 35: smi match: CS(C)~O CS(C)~O 35: smi match: CS(C)(~O)~O CS(C)(~O)~O 35: smi match: CS(N)(~O)~O CS(N)(~O)~O 35: smi match: CS([OH])(~O)~O CS([OH])(~O)~O 35: smi match: COS(C)(~O)~O COS(C)(~O)~O 35: smi match: *S(C)(~O)~O *S(C)(~O)~O 35: smi match: CN(C)C CN(C)C 35: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 35: smi match: *C(*)=S *C(*)=S 35: smi match: *OC(*)=S *OC(*)=S 33: [07:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors 73: [07:34:57] skipping block at line 7: 'BEGIN ATOM' 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 144 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp 73: Failed Expression: dp_inStream 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 179 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp 73: Failed Expression: dp_inStream 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 427 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp 73: Failed Expression: dp_inStream 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 274 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp 73: Failed Expression: dp_inStream 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 515 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 73: Failed Expression: dp_sInStream != nullptr 73: **** 73: 73: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 21 73: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 20 73: [07:34:57] 73: 73: **** 73: Post-condition Violation 73: Element '' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [07:34:57] BEGIN SGROUP line not found on line 14 73: [07:34:57] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. 73: [07:34:57] END SGROUP line not found on line 14 73: [07:34:57] END SGROUP line not found on line 14 73: [07:34:57] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. 73: [07:34:57] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. 73: [07:34:57] 73: 73: **** 73: Range Error 73: idx 73: Violation occurred on line 328 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: 99 < 9 73: **** 73: 73: [07:34:57] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. 73: [07:34:57] Multiple ATTCHPT values for atom 2 on line 9 73: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 12 73: [07:34:57] SMARTS Parse Error: syntax error while parsing: [#6;R 73: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' 73: [07:34:57] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. 73: [07:34:57] Skipping empty SMARTS value for SMARTSQ. 73: [07:34:57] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. 73: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 12 75: Randomness seeded to: 2209681215 75: =============================================================================== 75: All tests passed (100 assertions in 2 test cases) 75: 42/223 Test #75: XYZFileParserCatchTest ................. Passed 0.07 sec 58: [07:34:57] w block attempts to set wedging on bond 0 more than once. 58: [07:34:57] improperly formatted w block 58: [07:34:57] atom 3 is not associated with bond 1 in w block 58: =============================================================================== 58: All tests passed (1516 assertions in 53 test cases) 58: 25: done 43/223 Test #25: testUFFForceField ...................... Passed 0.25 sec 77: Randomness seeded to: 2285883672 77: [07:34:57] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 77: [07:34:57] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 77: [07:34:57] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 77: [07:34:57] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 77: [07:34:57] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored 77: =============================================================================== 77: All tests passed (142 assertions in 6 test cases) 77: 44/223 Test #77: molfileStereoCatchTest ................. Passed 0.06 sec 29: ...... 29: ---------------------------------------------------------------------- 29: Ran 6 tests in 0.001s 29: 29: OK 57: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC 57: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' 57: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON 57: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' 57: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 57: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 78: Randomness seeded to: 3254685953 78: =============================================================================== 78: All tests passed (8 assertions in 1 test case) 78: 45/223 Test #78: connectTheDotsTest ..................... Passed 0.05 sec 79: ----------------- Test 1 79: Done 79: 79: ----------------- Test 2 79: Done 79: 79: ----------------- Test 3 79: Done 79: 79: ----------------- Test 4 79: Done 79: 79: ----------------- Test 5 79: Done 79: 79: ----------------- Test 5 QueryRoot 79: Done 79: 79: ----------------- Test 6 (Issue71 related) 79: Done 79: 79: ----------------- Testing serial numbers on recursive queries 79: Done 79: 79: [07:34:57] ------------------------------------- 79: [07:34:57] Test multithreading 79: reading molecules 66: [07:34:57] Finished: testMae() 66: [07:34:57] ----------------------------------------- 66: 66: [07:34:57] 66: ----------------------------------------- 66: [07:34:57] Finished: testTdt() 66: [07:34:57] ----------------------------------------- 66: 54: --C1CCC2(CC1)CCCCC2CCC1CCCC1 46/223 Test #14: pySparseIntVect ........................ Passed 0.27 sec 47/223 Test #15: pyFPB .................................. Passed 0.27 sec 48/223 Test #57: smaTest1 ............................... Passed 0.16 sec test 84 Start 84: testEnumeration 84: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 84: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 84: Test timeout computed to be: 1500 test 85 Start 85: rxnTestCatch 85: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 85: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 85: Test timeout computed to be: 1500 test 86 Start 86: pyChemReactions 86: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 86: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 86: Test timeout computed to be: 1500 test 87 Start 87: pyChemReactionEnumerations 87: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 87: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 87: Test timeout computed to be: 1500 test 88 Start 88: pyChemReactionSanitize 88: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 88: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 88: Test timeout computed to be: 1500 test 89 Start 89: testChemTransforms 89: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 89: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms 89: Test timeout computed to be: 1500 test 90 Start 90: chemTransformsTestCatch 90: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms 90: Test timeout computed to be: 1500 35: smi match: * * 35: smi match: C[SH] C[SH] 35: smi match: c[SH] c[SH] 35: smi match: NC(N)=S NC(N)=S 35: smi match: * * 35: smi match: ***** ***** 35: smi match: NC(N)=O NC(N)=O 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing sf.net issue 280. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing sf.net issue 285. 35: [07:34:57] done 35: [07:34:57] done 35: [07:34:57] done 35: [07:34:57] done 35: [07:34:57] done 35: [07:34:57] done 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing Github2441: Add RDProps interface to Conformers. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing Issue2510: Pickle Confs as double. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing Github #2465: Negative atom-map numbers cause depickling to fail. 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing loading pickled mols with conformers 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing conformer reading/writing options 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing property reading options 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing property reading options 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing boost::serialization integration 35: [07:34:57] done 35: [07:34:57] ------------------------------------- 35: [07:34:57] Testing github issue 6036 73: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 73: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 73: [07:34:57] WARNING: Skipping property bar because the value includes an illegal blank line 73: [07:34:57] WARNING: Skipping property baz because the value includes an illegal blank line 73: [07:34:57] WARNING: Skipping property bletch 73: nope because the name includes a newline 73: [07:34:57] WARNING: Skipping property bletch 73: nope2 because the name includes a newline 73: [07:34:57] 73: 73: **** 73: Post-condition Violation 73: Element 'QQQ' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Post-condition Violation 73: Element 'QQQ' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Post-condition Violation 73: Element 'QQQ' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Post-condition Violation 73: Element 'QQQ' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [07:34:57] atom 3 has a negative isotope value. line: 15 73: [07:34:57] 73: 73: **** 73: Invariant Violation 73: bad prop value 73: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 73: Failed Expression: nSwaps < 2 73: **** 73: 73: [07:34:57] 73: 73: **** 73: Pre-condition Violation 73: no input stream 73: Violation occurred on line 480 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 73: Failed Expression: dp_sInStream 73: **** 73: 49/223 Test #58: smiTestCatch ........................... Passed 0.18 sec 19: ........... 19: ---------------------------------------------------------------------- 19: Ran 11 tests in 0.026s 19: 19: OK 19: Testing Geometry wrapper 50/223 Test #66: testGeneralFileReader .................. Passed 0.15 sec 54: smi: ClC1CCCCC1 54: smi: ClC1CCCCC1 54: smi: ClC1CCCCC1Br 54: smi: c1ccccc1 54: smi: c1ccncc1 54: smi: c1cc[nH]c1 54: smi: c1cc[nH]c1 54: smi: c1cc[pH]c1 76: Randomness seeded to: 2719823162 76: [07:34:57] Invalid or missing fragment id from CDXML fragment, assigning new one... 76: [07:34:57] Explicit valence for atom # 3 N, 4, is greater than permitted 76: [07:34:57] CDXMLParser: failed sanitizing skipping fragment 32 76: [07:34:57] Bad bond in CDXML skipping fragment 58... 76: [07:34:57] Invalid or missing fragment id from CDXML fragment, assigning new one... 76: [07:34:57] Bad bond in CDXML skipping fragment 58... 61: Randomness seeded to: 2713940792 61: =============================================================================== 61: All tests passed (571 assertions in 14 test cases) 61: 65: [07:34:57] Finished: testMolSup() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testRandMolSup() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 83: [07:34:57] ------------------------------------- 83: [07:34:57] Test Reaction StructuralFingerprint 51/223 Test #13: pyDiscreteValueVect .................... Passed 0.29 sec 52/223 Test #23: pyAlignment ............................ Passed 0.28 sec 53/223 Test #35: graphmoltestPickler .................... Passed 0.25 sec 54/223 Test #61: depictorCatch .......................... Passed 0.16 sec test 91 Start 91: tautomerQueryTestCatch 91: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 91: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery 91: Test timeout computed to be: 1500 test 92 Start 92: pyTautomerQuery 92: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 92: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 92: Test timeout computed to be: 1500 test 93 Start 93: testSubgraphs1 93: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 93: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 93: Test timeout computed to be: 1500 test 94 Start 94: testSubgraphs2 94: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 94: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 94: Test timeout computed to be: 1500 test 95 Start 95: subgraphsCatch 95: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 95: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs 95: Test timeout computed to be: 1500 test 96 Start 96: filterCatalogTest 96: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog 96: Test timeout computed to be: 1500 54: CbC(aC)aC 54: CaC(bC)aC 54: CbC(bC)aC 54: O.C 54: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O 54: [07:34:57] SMILES Parse Error: syntax error while parsing: c%()ccccc%() 54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' 54: [07:34:57] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) 54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' 54: [07:34:57] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' 54: [07:34:57] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' 54: [07:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [07:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [07:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [07:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [07:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [07:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: C=c1s/c2n(c1=O)CCCCCCC\N=2 54: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 54: [07:34:57] SMILES Parse Error: extra close parentheses while parsing: C) 54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 76: [07:34:57] WARNING: not removing hydrogen atom without neighbors 83: [07:34:57] ------------------------------------- 83: [07:34:57] Test Reaction DifferenceFingerprint 55/223 Test #3: pyCoordGen ............................. Passed 0.33 sec 79: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 79: processing 79: launch :0 79: launch :1 79: launch :2 79: launch :3 82: smi: O=C1CNC(=O)CN1 82: 1: O=C1CNC(=O)CN1 82: 2: COOC 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 82: O=C1CNC(=O)CN1 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 4 82: [07:34:57] atom 0 in product 0 has multiple charge specifications. 82: mass: 15.0001 82: Oc1ccccn1 82: Oc1ccc[nH]1 93: ----------------------- 93: Subgraph retrieval 93: Finished 93: ----------------------- 93: testSubgraphs2a 56/223 Test #29: pyDistGeom ............................. Passed 0.29 sec 57/223 Test #54: smiTest1 ............................... Passed 0.21 sec 58/223 Test #83: testReactionFingerprints ............... Passed 0.05 sec test 97 Start 97: pyFilterCatalog 97: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 97: Test timeout computed to be: 1500 test 98 Start 98: testFragCatalog 98: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog 98: Test timeout computed to be: 1500 test 99 Start 99: pyFragCatalog 99: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 99: Test timeout computed to be: 1500 test 100 Start 100: testDescriptors 100: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 100: Test timeout computed to be: 1500 76: [07:34:57] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. 76: [07:34:57] Incomplete atom labelling, cannot make bond 76: [07:34:57] Incomplete atom labelling, cannot make bond 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: ([C:2] 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:2]) 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' 82: [07:34:57] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 82: [07:34:57] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 82: [07:34:57] reactant 2 has no mapped atoms. 82: [07:34:57] >> Atoms within one molecule have different RXN roles. 82: [07:34:57] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: ([C:2] 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' 82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] 82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' 93: Finished 93: ----------------------- 93: testSubgraphs2 94: ----------------------- 94: Test1: pathToSubmol 94: Finished 94: ----------------------- 94: Test2: Atom Environments 94: Finished 94: ----------------------- 94: Test 3: Atom Environments (Extension) 94: Finished 94: ----------------------- 94: Testing github Issue103: stereochemistry and pathToSubmol 94: Finished 94: ----------------------- 94: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 94: Finished 89: 1 smi: CC 89: 1 smi: CC 89: 2 smi: CCO[C@H](N)P 89: 2 smi: CC 89: replaceSub smi1:CCP(CC)[C@@H](N)O 89: replaceSub smi1:CCNCC 89: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 89: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O 89: [07:34:57] SMARTS Parse Error: syntax error while parsing: bar 89: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' 65: [07:34:57] Finished: testSmilesSup() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] ------------------------------------------------------ 65: [07:34:57] SMILES Parse Error: syntax error while parsing: fail 65: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 65: [07:34:57] ERROR: Smiles parse error on line 3 65: [07:34:57] ERROR: Cannot create molecule from : 'fail' 65: [07:34:57] ------------------------------------------------------ 65: [07:34:57] ------------------------------------------------------ 65: [07:34:57] >>> This may result in an infinite loop. It should finish almost immediately: 65: [07:34:57] <<< done. 65: [07:34:57] Finished: testSmilesSupFromText() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testSmilesWriter() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 95: Randomness seeded to: 2870800801 95: --------- 95: =============================================================================== 95: All tests passed (11 assertions in 1 test case) 95: 85: Randomness seeded to: 3603752063 85: [07:34:57] atom 0 in product 0 has multiple charge specifications. 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 34 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 36 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 38 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 40 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 42 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 87 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 89 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 91 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 93 85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 95 90: Randomness seeded to: 1287606086 90: [07:34:57] Incomplete atom labelling, cannot make bond 90: [07:34:57] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 59/223 Test #94: testSubgraphs2 ......................... Passed 0.03 sec 60/223 Test #95: subgraphsCatch ......................... Passed 0.03 sec test 101 Start 101: testAUTOCORR2D 101: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 test 102 Start 102: testATF 102: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF 102: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 82: [07:34:57] reactant 0 has no mapped atoms. 82: [07:34:57] reactant 1 has no mapped atoms. 82: [07:34:57] reactant 3 has no mapped atoms. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 5 found multiple times. 82: [07:34:57] product atom-mapping number 6 found multiple times. 82: [07:34:57] product atom-mapping number 7 found multiple times. 82: [07:34:57] product atom-mapping number 8 found multiple times. 82: [07:34:57] product atom-mapping number 12 found multiple times. 82: [07:34:57] product atom-mapping number 9 found multiple times. 82: [07:34:57] product atom-mapping number 10 found multiple times. 82: [07:34:57] product atom-mapping number 11 found multiple times. 82: [07:34:57] reactant 0 has no mapped atoms. 82: [07:34:57] reactant 1 has no mapped atoms. 82: [07:34:57] reactant 3 has no mapped atoms. 82: [07:34:57] reactant atom-mapping number 19 found multiple times. 82: [07:34:57] reactant atom-mapping number 25 found multiple times. 82: [07:34:57] reactant atom-mapping number 20 found multiple times. 82: [07:34:57] reactant atom-mapping number 21 found multiple times. 82: [07:34:57] reactant atom-mapping number 22 found multiple times. 82: [07:34:57] reactant atom-mapping number 23 found multiple times. 82: [07:34:57] reactant atom-mapping number 24 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 82: [07:34:57] product atom-mapping number 5 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 5 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 82: [07:34:57] product atom-mapping number 5 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 5 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: F[C@@](Cl)(Br)O[C@](F)(Cl)Br 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: F[C@](Cl)(Br)O[C@](F)(Cl)Br 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 4 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 4 82: [07:34:57] product atom-mapping number 3 found multiple times. 82: [07:34:57] product atom-mapping number 2 found multiple times. 82: [07:34:57] product atom-mapping number 1 found multiple times. 82: [07:34:57] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 4 82: [07:34:57] product atom-mapping number 6 not found in reactants. 82: [07:34:57] product atom-mapping number 7 not found in reactants. 82: [07:34:57] product atom-mapping number 8 not found in reactants. 82: [07:34:57] product atom-mapping number 7 not found in reactants. 82: [07:34:57] product atom-mapping number 8 not found in reactants. 82: [07:34:57] product atom-mapping number 9 not found in reactants. 82: [07:34:57] product atom-mapping number 10 not found in reactants. 82: [07:34:57] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 6 82: [07:34:57] product atom-mapping number 7 not found in reactants. 82: [07:34:57] product atom-mapping number 8 not found in reactants. 82: [07:34:57] product atom-mapping number 9 not found in reactants. 82: [07:34:57] product atom-mapping number 10 not found in reactants. 82: [07:34:57] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 6 65: [07:34:57] Finished: testSDWriter() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testSDSupplierEnding() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testSuppliersEmptyFile() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testCisTrans() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testStereoRound() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 65: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 65: [07:34:57] Finished: testIssue226() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 85: [07:34:57] mapped atoms in the reactants were not mapped in the products. 85: unmapped numbers are: 2 85: [07:34:57] mapped atoms in the reactants were not mapped in the products. 85: unmapped numbers are: 2 85: [07:34:57] SMARTS Parse Error: unclosed ring for input: 'CC1' 85: [07:34:57] SMILES Parse Error: unclosed ring for input: 'CC1' 85: [07:34:57] mapped atoms in the reactants were not mapped in the products. 85: unmapped numbers are: 2 85: [07:34:57] product atom-mapping number 2 not found in reactants. 85: [07:34:57] mapped atoms in the reactants were not mapped in the products. 85: unmapped numbers are: 2 85: [07:34:57] product atom-mapping number 2 not found in reactants. 90: [07:34:57] Incomplete atom labelling, cannot make bond 90: [07:34:57] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 61/223 Test #19: testPyGeometry ......................... Passed 0.34 sec test 103 Start 103: testBCUT 103: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 82: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 82: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 65: [07:34:57] Finished: testTDTSupplier1() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testTDTSupplier2() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testTDTSupplier3() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testSDSupplierFromText() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] ERROR: Problems encountered parsing data fields 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] ERROR: Problems encountered parsing data fields 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] Spurious data before the first property will be ignored 65: [07:34:57] Property will be truncated after the first blank line 65: [07:34:57] Property will be truncated after the first blank line 65: [07:34:57] Property will be truncated after the first blank line 65: [07:34:57] Finished: testSDSupplierStrLax1() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] ERROR: Problems encountered parsing data fields 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] Property will be truncated after the first blank line 65: [07:34:57] Finished: testSDSupplierStrLax2() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] ERROR: Problems encountered parsing data fields 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] ERROR: Problems encountered parsing data fields 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] Spurious data before the first property will be ignored 65: [07:34:57] Property will be truncated after the first blank line 65: [07:34:57] Property will be truncated after the first blank line 65: [07:34:57] Property will be truncated after the first blank line 65: [07:34:57] Finished: testSDSupplierFromTextStrLax1() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] ERROR: Problems encountered parsing data fields 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] Property will be truncated after the first blank line 65: [07:34:57] Finished: testSDSupplierFromTextStrLax2() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testIssue265() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] ERROR: End of data field name not found 65: [07:34:57] ERROR: moving to the beginning of the next molecule 85: [07:34:57] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 73: [07:34:57] ERROR: molecules without atoms cannot be exported to Maestro files. 73: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 73: [07:34:57] ERROR: the mol cannot be kekulized, and will not be written to the output file. 73: [07:34:57] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. 73: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 73: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 73: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test Crippen parameter acquisition. 65: [07:34:57] Explicit valence for atom # 0 F, 2, is greater than permitted 65: [07:34:57] ERROR: Could not sanitize molecule ending on line 16 65: [07:34:57] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted 73: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 65: [07:34:57] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] ERROR: Bond line too short: 'M END' on line 18 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] Finished: testSDErrorHandling() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 73: =============================================================================== 73: All tests passed (1311 assertions in 87 test cases) 73: 76: [07:34:57] Incomplete atom labelling, cannot make bond 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test Crippen calculation. 85: =============================================================================== 85: All tests passed (568 assertions in 20 test cases) 85: 98: 21 62/223 Test #73: fileParsersCatchTest ................... Passed 0.18 sec 63/223 Test #85: rxnTestCatch ........................... Passed 0.09 sec test 104 Start 104: testEEM 104: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM 104: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 104: Test timeout computed to be: 1500 test 105 Start 105: testPBF 105: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF 105: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 105: Test timeout computed to be: 1500 65: [07:34:57] Finished: testIssue381() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testSetStreamIndices() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testMixIterAndRandom() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: build: 65: [07:34:57] Finished: testRemoveHs() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 90: [07:34:57] Incomplete atom labelling, cannot make bond 90: [07:34:57] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 90: [07:34:57] Incomplete atom labelling, cannot make bond 90: [07:34:57] Incomplete atom labelling, cannot make bond 90: [07:34:57] Incomplete atom labelling, cannot make bond 90: [07:34:57] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test Issue262: problems with Crippen calculation from pickles. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test AMW calculation. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test Exact MW calculation. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test Labute ASA descriptors. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test TPSA descriptors. 101: [07:34:57] ---------------------------- 101: start test autocorr2D 103: [07:34:57] ------------------------------------- 103: [07:34:57] Basic BCUT tests. 76: [07:34:57] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 76: [07:34:57] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 64/223 Test #89: testChemTransforms ..................... Passed 0.09 sec 65/223 Test #102: testATF ................................ Passed 0.03 sec test 106 Start 106: testRDFcustom 106: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 106: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 106: Test timeout computed to be: 1500 test 107 Start 107: testRDF 107: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF 107: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 107: Test timeout computed to be: 1500 65: [07:34:57] Finished: testGetItemText() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 90: [07:34:57] Incomplete atom labelling, cannot make bond 90: [07:34:57] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 90: [07:34:57] 90: 90: **** 90: Invariant Violation 90: molzip: zipped Bond already exists, perhaps labels are duplicated 90: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) 90: **** 90: 103: [07:34:57] done 103: [07:34:57] ------------------------------------- 103: [07:34:57] Larger BCUT tests. 76: [07:34:57] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast 76: [07:34:57] Failed to parse XML fragment 5 node: b attribute: Order: 5 76: =============================================================================== 76: All tests passed (252 assertions in 4 test cases) 76: 82: [07:34:57] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 105: [07:34:57] ------------------------------------- 105: [07:34:57] Basic PBF tests. 66/223 Test #76: cdxmlParserCatchTest ................... Passed 0.19 sec test 108 Start 108: testMORSE 108: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 108: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 108: Test timeout computed to be: 1500 65: [07:34:57] Finished: testForwardSDSupplier() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testMissingCRSDSupplier() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testIssue3482695() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 90: =============================================================================== 90: All tests passed (667 assertions in 7 test cases) 90: 27: ...[07:34:57] Molecule does not have explicit Hs. Consider calling AddHs() 67/223 Test #90: chemTransformsTestCatch ................ Passed 0.11 sec test 109 Start 109: test3D 109: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D 109: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 109: Test timeout computed to be: 1500 65: [07:34:57] ERROR: Cannot convert 'foo' to unsigned int on line 557 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] Finished: testIssue3525673() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testBlankLinesInProps() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testSkipLines() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testGitHub23() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testGitHub88() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 27: [07:34:57] 27: 27: **** 27: Invariant Violation 27: bad direction in linearSearch 27: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h 27: Failed Expression: status >= 0 27: **** 27: 104: =>start test EEM 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: 0 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 96: Warning: molecule failed filter 96: Warning: molecule failed filter: reason hzone_phenol_A(479) 96: v = { 96: 0,23}, 96: 1,22}, 96: 2,20}, 96: 3,19}, 96: 4,25}, 96: 5,24}, 96: 6,18}, 96: 7,17}, 96: 8,16}, 96: 9,21}, 96: } 96: match = { 96: 0,23}, 96: 1,22}, 96: 2,20}, 96: 3,19}, 96: 4,25}, 96: 5,24}, 96: 6,18}, 96: 7,17}, 96: 8,16}, 96: 9,21}, 96: } 96: Warning: molecule failed filter 96: Warning: molecule failed filter: reason cyano_imine_B(17) 96: v = { 96: 0,11}, 96: 1,12}, 96: 2,13}, 96: 3,14}, 96: 4,15}, 96: 5,10}, 96: 6,9}, 96: 7,8}, 96: 8,7}, 96: 9,6}, 96: 10,5}, 96: 11,17}, 96: 12,16}, 96: } 96: match = { 96: 0,11}, 96: 1,12}, 96: 2,13}, 96: 3,14}, 96: 4,15}, 96: 5,10}, 96: 6,9}, 96: 7,8}, 96: 8,7}, 96: 9,6}, 96: 10,5}, 96: 11,17}, 96: 12,16}, 96: } 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 93: Finished 93: ----------------------- 93: Path retrieval 93: Finished 93: ----------------------- 93: Path retrieval2 93: Finished 93: ----------------------- 93: Unique Subgraph retrieval 93: Finished 93: ----------------------- 93: testUniqueSubgraphs2 96: Warning: molecule failed filter 84: 30000000 30000000 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 96: Warning: molecule failed filter: reason keto_keto_gamma(5) 96: v = { 96: 0,0}, 96: 1,1}, 96: 2,2}, 96: 3,4}, 96: 4,5}, 96: 5,6}, 96: 6,7}, 96: 7,8}, 96: 8,9}, 96: 9,14}, 96: 10,15}, 96: 11,16}, 96: } 96: match = { 96: 0,0}, 96: 1,1}, 96: 2,2}, 96: 3,4}, 96: 4,5}, 96: 5,6}, 96: 6,7}, 96: 7,8}, 96: 8,9}, 96: 9,14}, 96: 10,15}, 96: 11,16}, 96: } 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 82: [07:34:57] product atom-mapping number 17 not found in reactants. 82: [07:34:57] product atom-mapping number 18 not found in reactants. 82: [07:34:57] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 12 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 65: [07:34:57] Finished: testGitHub2285() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 65: [07:34:57] ERROR: Smiles parse error on line 1 65: [07:34:57] ERROR: Cannot create molecule from : 'c1ccccc' 65: [07:34:57] SMILES Parse Error: extra open parentheses for input: 'C(C' 4: dynamic boost any:0.355241 s 65: [07:34:57] ERROR: Smiles parse error on line 3 65: [07:34:57] ERROR: Cannot create molecule from : 'C(C' 65: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted 65: [07:34:57] ERROR: Could not sanitize molecule on line 5 65: [07:34:57] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 65: [07:34:57] Explicit valence for atom # 1 F, 2, is greater than permitted 65: [07:34:57] ERROR: Could not sanitize molecule ending on line 21 65: [07:34:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 65: [07:34:57] Explicit valence for atom # 1 F, 2, is greater than permitted 65: [07:34:57] ERROR: Could not sanitize molecule ending on line 21 65: [07:34:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 65: [07:34:57] Explicit valence for atom # 1 F, 2, is greater than permitted 65: [07:34:57] ERROR: Could not sanitize molecule ending on line 21 65: [07:34:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 65: [07:34:57] ERROR: Atom line too short: ' -9.6' on line 28 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] Explicit valence for atom # 1 F, 2, is greater than permitted 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 65: [07:34:57] ERROR: Could not sanitize molecule ending on line 21 65: [07:34:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 65: [07:34:57] ERROR: Atom line too short: ' -9.6' on line 28 65: [07:34:57] ERROR: moving to the beginning of the next molecule 65: [07:34:57] Finished: testGitHub2479() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] 65: 65: **** 65: Invariant Violation 65: bad chiral bond 65: Violation occurred on line 164 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 65: Failed Expression: bnd 65: **** 65: 65: [07:34:57] Finished: testGitHub2881() 65: [07:34:57] ----------------------------------------- 65: 65: [07:34:57] ----------------------------------------- 65: [07:34:57] Finished: testGitHub3517() 65: [07:34:57] ----------------------------------------- 65: 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 109: [07:34:57] ------------------------------------- 109: [07:34:57] Basic PMI tests. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68/223 Test #65: testMolSupplier ........................ Passed 0.28 sec test 110 Start 110: testWHIM 110: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 110: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 110: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: [07:34:57] bond with order 0 found on line 11. This is not part of the MDL specification. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: [07:34:57] bond with order 0 found on line 16. This is not part of the MDL specification. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 60: [07:34:57] Warning: stereochemistry around double bond may be incorrect in depiction. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: lostStereoAnd.sdf 63: 63: Test 63: 63: DoubleBondChain.sdf 63: 63: Test 63: 63: UnitsError.sdf 63: 63: Test 63: 63: StarAtom.sdf 63: 63: Test 63: 63: nonProprietary.mol 63: 63: Test 63: 63: ChiralTest.sdf 63: 63: Test 63: 63: TestBond1.mol 63: 63: Test 63: 63: Sgroup_MUL_ParentInMiddle.sdf 63: 63: Test 63: 63: Cubane.mrv 63: 63: Test 63: 63: NewChiralTest.mrv 63: 63: Test 63: 63: NewChiralTest.mrv 63: 63: Test 63: 63: NewChiralTestNoChiral.mrv 63: 63: Test 63: 63: NewChiralTestNoChiral.mrv 63: 63: Test 63: 63: NewChiralTestAllChiral.mrv 63: 63: Test 63: 63: NewChiralTestAllChiral.mrv 63: 63: Test 63: 63: lostStereoAnd.mrv 63: 63: Test 63: 63: DoubleBondChain.mrv 63: 63: Test 63: 63: WigglyAndCrossed.mrv 63: 63: Test 63: 63: BondTypes.mrv 63: 63: Test 63: 63: EmbeddedSGroupSUP_MUL.mrv 63: 63: Test 63: 63: EmbeddedSgroupCOP_SUP.mrv 63: 63: Test 63: 63: EmbeddedSgroupDAT_SUP.mrv 63: 63: Test 63: 63: EmbeddedSgroupMULTICENTER_SUP.mrv 63: 63: Test 63: 63: EmbeddedSgroupMUL_MUL.mrv 63: 63: Test 63: 63: EmbeddedSgroupMUL_MUL2.mrv 63: 63: Test 63: 63: EmbeddedSgroupMUL_SUP.mrv 63: 63: Test 63: 63: EmbeddedSgroupSRU_SUP.mrv 63: 63: Test 63: 63: EmbeddedSgroupSUPEXP_SUP.mrv 63: 63: Test 63: 63: EmbeddedSgroupSUPEXP_SUP2.mrv 63: 63: Test 63: 63: EmbeddedSgroupSUP_MULTICENTER.mrv 63: 63: Test 63: 63: EmbeddedSgroupSUP_SUP.mrv 63: 63: Test 63: 63: EmbeddedSgroupSUP_SUP2.mrv 63: 63: Test 63: 63: RgroupBad.mrv 63: 63: Test 63: 63: valenceLessThanDrawn.mrv 63: 63: Test 63: 63: data_sgroup_no_fieldname.mrv 63: 63: Test 63: 63: data_sgroup_empty_field_data.mrv 63: 63: Test 63: 63: radical_value.mrv 63: 63: Test 63: 63: emptyOneLineAtomList.mrv 63: 63: Test 63: 63: mrvValence_value.mrv 63: 63: Test 63: 63: ChiralTest2.mrv 63: 63: Test 63: 63: ChiralTest.mrv 63: 63: Test 63: 63: SnCl2.mrv 63: 63: Test 63: 63: SnH2Cl2.mrv 63: 63: Test 63: 63: marvin01.mrv 63: 63: Test 63: 63: marvin02.mrv 63: 63: Test 63: 63: marvin07.mrv 63: 63: Test 63: 63: marvin10.mrv 63: 63: Test 63: 63: marvin06.mrv 63: 63: Test 63: 63: marvin12.mrv 63: 63: Test 63: 63: EmptyMol.mrv 63: 63: Test 63: 63: Sparse.mrv 63: 63: Test 63: 63: Sparse2.mrv 63: 63: Test 63: 63: Sparse3.mrv 63: 63: Test 63: 63: MarvinNoCoords.mrv 63: 63: Test 63: 63: aspirin.mrv 63: 63: Test 63: 63: MarvinStereoGroupsZeros.mrv 63: 63: Test 63: 63: MarvinStereoGroupsAbs.mrv 63: 63: Test 63: 63: triphenylphosphine.mrv 63: 63: Test 63: 63: MarvinOldSuperGroupTest.mrv 63: 63: Test 63: 63: RadicalTests.mrv 63: 63: Test 63: 63: AnyBond.mrv 63: 63: Test 63: 63: cisBenzene.mrv 63: 63: Test 63: 63: DativeBond.mrv 63: 63: Test 63: 63: MultipleSgroup.mrv 63: 63: Test 63: 63: SgroupExpanded.mrv 63: 63: Test 63: 63: SgroupMultAttach.mrv 63: 63: Test 63: 63: MarvinMissingX2.mrv 63: 63: Test 63: 63: MarvinMissingY2.mrv 63: 63: Test 63: 63: DataSgroup.mrv 63: 63: Test 63: 63: MulticenterSgroup.mrv 63: 63: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 63: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test Lipinski parameters. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69/223 Test #68: testMolWriter .......................... Passed 0.29 sec test 111 Start 111: testGETAWAY 111: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 111: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 63: Test 63: 63: GenericSgroup.mrv 63: 63: Test 63: 63: MonomerSgroup.mrv 63: 63: Test 63: 63: modification_sgroup.mrv 63: 63: Test 63: 63: copolymer_sgroup.mrv 63: 63: Test 63: 63: MultipleSgroupParentInMiddleOfAtomBlock.mrv 63: 63: Test 63: 63: EmbeddedSgroups.mrv 63: 63: Test 63: 63: marvin03.mrv 63: 63: Test 63: 63: MarvinBadMissingMolID.mrv 63: 63: [07:34:57] 63: 63: **** 63: Test Assert 63: Expression Failed: 63: Violation occurred on line 309 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp 63: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr 63: **** 63: 63: Test 63: 63: MarvinBadMissingAtomID.mrv 63: 63: Expected id, elementType for an atom definition in MRV file 63: Test 63: 63: MarvinBadX2.mrv 63: 63: The values x2 and y2 must be large floats in MRV file 63: Test 63: 63: MarvinBadY2.mrv 63: 63: The values x2 and y2 must be large floats in MRV file 63: Test 63: 63: MarvinBadStereoGroupsAbs.mrv 63: 63: Unrecognized group definition 63: Test 63: 63: MarvinBadElementType.mrv 63: 63: Test 63: 63: MarvinBadMissingBondID.mrv 63: 63: Test 63: 63: MarvinBadMissingBondAtomRefs 63: 63: Test 63: 63: MarvinBadMissingBondOrder.mrv 63: 63: bond must have one of: order, queryType, or convention in MRV File 63: Test 63: 63: MarvinBadMissingSruMolID.mrv 63: 63: Expected a molID in MRV file 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadMissingSruID.mrv 63: 63: Test 63: 63: MarvinBadMissingSruRole.mrv 63: 63: Test 63: 63: MarvinBadMissingSruAtomRef.mrv 63: 63: Test 63: 63: MarvinBadMissingSruTitle.mrv 63: 63: Test 63: 63: MarvinBadSruAtomRef.mrv 63: 63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSruID.mrv 63: 63: Test 63: 63: MarvinBadSruRole.mrv 63: 63: Test 63: 63: MarvinBadSruAtomRef.mrv 63: 63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSruAtomRef.mrv 63: 63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 79: done 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 79: processing2 79: launch2 :0 63: Test 63: 63: MarvinBadSruConnect.mrv 63: 63: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file 79: launch2 :1 79: launch2 :2 79: launch2 :3 63: Test 63: 63: MarvinBadSupAttachAtom.mrv 63: 63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 63: Test 63: 63: MarvinBadSupAttachBond.mrv 63: 63: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 4: static RDAny:0.050281 s 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupAttachOrder.mrv 63: 63: Order for an AttachmentPoint definition must be an integer in MRV file 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupAttachAtom.mrv 63: 63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupAttachAtom.mrv 63: 63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupAttachAtom.mrv 63: 63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupMissingAttachBond.mrv 63: 63: No attachment point found for bond to the condensed atom in a superatomSgroup 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupMissingAttachOrder.mrv 63: 63: Expected atom, order and bond, for an AttachmentPoint definition in MRV file 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 82: [07:34:57] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 82: [07:34:57] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 82: 82: [07:34:57] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 82: ------------- 82: CCOc1ccccc1 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: done 79: preprocessing 3 91: Randomness seeded to: 3317144408 91: =============================================================================== 91: All tests passed (93 assertions in 13 test cases) 91: 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 79: processing3 79: launch3 :0 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70/223 Test #91: tautomerQueryTestCatch ................. Passed 0.21 sec test 112 Start 112: testAUTOCORR3D 112: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 112: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: launch3 :1 79: launch3 :2 79: launch3 :3 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 71/223 Test #60: testDepictor ........................... Passed 0.39 sec test 113 Start 113: testCoulombMat 113: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 113: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: marvin03.mrv 63: 63: Test 63: 63: AlexRxn.mrv 63: 63: Test 63: 63: BadReactionSign.mrv 63: 63: Test 63: 63: bondArray_node.mrv 63: 63: Test 63: 63: marvin03.mrv 63: 63: Test 63: 63: marvin04.mrv 63: 63: Test 63: 63: marvin08.mrv 63: 63: Test 63: 63: marvin09.mrv 63: 63: Test 63: 63: marvin11.mrv 63: 63: Test 63: 63: marvin05.mrv 63: 63: Test 63: 63: EmptyRxn.mrv 63: 63: [07:34:57] initialization failed 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: 100 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: ===================== Testing CoulombMat ======================= 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: CM test 1 mat Done 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 72/223 Test #113: testCoulombMat ......................... Passed 0.04 sec test 114 Start 114: descriptorsTestCatch 114: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 114: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 114: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: RxnNoCoords.mrv 63: 63: Test 63: 63: mrvValenceZero.mrv 63: 63: Test 63: 63: condition_coordinates_mpoint.mrv 63: 63: Test 63: 63: marvin01.mrv 63: 63: Test 63: 63: aspirineSynthesisWithAttributes.mrv 63: 63: Test 63: 63: marvin01.mrv 63: 63: Test 63: 63: NewChiralTest 63: 63: Test 63: 63: NewChiralTest 63: 63: Test 63: 63: NewChiralTestNoChiral 63: 63: Test 63: 63: NewChiralTestNoChiral 63: 63: Test 63: 63: NewChiralTest2 63: 63: Test 63: 63: NewChiralTest2 63: 63: Test 63: 63: NewChiralTest2AllChiral 63: 63: Test 63: 63: NewChiralTest2AllChiral 63: 63: Test 63: 63: DoubleBondChain 63: 63: Test 63: 63: Na_Mg_Al_OH 63: 63: Test 63: 63: Pb 63: 63: Test 63: 63: O_Mg_Si 63: 63: Test 63: 63: SquiggleBond 63: 63: Test 63: 63: BigMacrocycle 63: 63: Test 63: 63: Smiles1 63: 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 73/223 Test #63: testMrvToMol ........................... Passed 0.43 sec test 115 Start 115: pyMolDescriptors 115: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 115: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap 115: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test VSA descriptors. 74/223 Test #96: filterCatalogTest ...................... Passed 0.28 sec test 116 Start 116: pyMolDescriptors3D 116: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/test3D.py" 116: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap 116: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test molecular formula calculation. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test Issue 3415534. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test Issue3433771: Bad definition for Crippen atom type O11. 100: [07:34:57] done 100: [07:34:57] ------------------------------------- 100: [07:34:57] Test multithreading 100: reading molecules 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 93: Finished 93: ----------------------- 93: testRootedSubgraphs 93: Finished 93: ----------------------- 93: testRootedPaths 93: Finished 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 75/223 Test #93: testSubgraphs1 ......................... Passed 0.31 sec test 117 Start 117: testFingerprints 117: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 117: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 100: processing 100: launch :0 100: launch :1 100: launch :2 100: launch :3 87: [07:34:57] == testCartesianProduct 80: Randomness seeded to: 1794068580 80: =============================================================================== 80: All tests passed (143 assertions in 7 test cases) 80: 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 92: ..... 92: ---------------------------------------------------------------------- 92: Ran 5 tests in 0.043s 92: 92: OK 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 76/223 Test #80: substructTestCatch ..................... Passed 0.37 sec test 118 Start 118: testMHFPFingerprint 118: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 118: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 88: .[07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 79: done 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 114: Randomness seeded to: 1126129511 114: =============================================================================== 114: All tests passed (482 assertions in 7 test cases) 114: 79: [07:34:57] done 79: [07:34:57] ------------------------------------- 79: [07:34:57] Test GitHub issue 15 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: [07:34:57] done 79: [07:34:57] ------------------------------------- 79: [07:34:57] Test GitHub issue 409 105: [07:34:57] done 105: [07:34:57] ------------------------------------- 105: [07:34:57] PBF edge cases. 79: [07:34:57] done 79: [07:34:57] ------------------------------------- 79: [07:34:57] Test chiral matching 77/223 Test #114: descriptorsTestCatch ................... Passed 0.08 sec test 119 Start 119: testFingerprintGenerators 119: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 119: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 119: Test timeout computed to be: 1500 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: [07:34:57] done 79: [07:34:57] ------------------------------------- 79: [07:34:57] Test GitHub issue 688: partially specified chiral substructure queries don't work properly 79: [07:34:57] done 79: [07:34:57] ------------------------------------- 79: [07:34:57] Test dative-bond matching 79: [07:34:57] done 79: [07:34:57] ------------------------------------- 79: [07:34:57] Test cis/trans matching 79: [07:34:57] done 79: [07:34:57] ------------------------------------- 79: [07:34:57] Test cis/trans matching part 2 79: [07:34:57] done 79: [07:34:57] ------------------------------------- 79: [07:34:57] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS 79: [07:34:57] done 118: [07:34:57] ------------------------------------- 118: [07:34:57] Test MHFP fingerprint encoder initialization 88: .[07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: () 88: ******************************************** 88: $RXN 88: 88: RDKit 88: 88: 2 1 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 1 0 0 0 0 0 0999 V2000 88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 88: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 1 2 1 0 88: M RGP 1 2 1 88: V 1 halogen.bromine.aromatic 88: V 2 [*:1] 88: M STY 1 1 DAT 88: M SAL 1 1 1 88: M SED 1 [#35&$([Br&$(Br-&!@c)])] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 4 3 0 1 0 0 0 0 0 0999 V2000 88: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 2 3 1 0 88: 1 2 1 0 88: 2 4 1 0 88: M RGP 1 1 2 88: V 1 [*:2] 88: V 2 boronicacid 88: M STY 1 1 DAT 88: M SAL 1 1 2 88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 0 0 0 0 0 0 0999 V2000 88: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 88: 1 2 1 0 88: M RGP 2 1 1 2 2 88: V 1 [*:1] 88: V 2 [*:2] 88: M END 88: 88: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 88: $RXN 88: 88: RDKit 88: 88: 2 1 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 1 0 0 0 0 0 0999 V2000 88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 88: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 1 2 1 0 88: M RGP 1 2 1 88: V 1 halogen.bromine.aromatic 88: V 2 [*:1] 88: M STY 1 1 DAT 88: M SAL 1 1 1 88: M SED 1 [#35&$([Br&$(Br-&!@c)])] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 4 3 0 1 0 0 0 0 0 0999 V2000 88: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 2 3 1 0 88: 1 2 1 0 88: 2 4 1 0 88: M RGP 1 1 2 88: V 1 [*:2] 88: V 2 boronicacid 88: M STY 1 1 DAT 88: M SAL 1 1 2 88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 0 0 0 0 0 0 0999 V2000 88: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 88: 1 2 1 0 88: M RGP 2 1 1 2 2 88: V 1 [*:1] 88: V 2 [*:2] 88: M END 88: 88: ******************************************** 88: $RXN 88: 88: RDKit 88: 88: 2 1 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 1 0 0 0 0 0 0999 V2000 88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 88: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 88: 1 2 1 0 88: M RGP 1 2 1 88: V 1 halogen.bromine.aromatic 88: V 2 * 88: M STY 1 1 DAT 88: M SAL 1 1 1 88: M SED 1 [#35&$([Br&$(Br-&!@c)])] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 4 3 0 1 0 0 0 0 0 0999 V2000 88: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 2 3 1 0 88: 1 2 1 0 88: 2 4 1 0 88: M RGP 1 1 2 88: V 1 * 88: V 2 boronicacid 88: M STY 1 1 DAT 88: M SAL 1 1 2 88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 0 0 0 0 0 0 0999 V2000 88: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 88: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 88: 1 2 1 0 88: M RGP 2 1 1 2 2 88: V 1 * 88: V 2 * 88: M END 88: 88: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 88: $RXN 88: 88: RDKit 88: 88: 2 1 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 1 0 0 0 0 0 0999 V2000 88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 88: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 1 2 1 0 88: M RGP 1 2 1 88: V 1 halogen.bromine.aromatic 88: V 2 [*:1] 88: M STY 1 1 DAT 88: M SAL 1 1 1 88: M SED 1 [#35&$([Br&$(Br-&!@c)])] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 4 3 0 1 0 0 0 0 0 0999 V2000 88: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 2 3 1 0 88: 1 2 1 0 88: 2 4 1 0 88: M RGP 1 1 2 88: V 1 [*:2] 88: V 2 boronicacid 88: M STY 1 1 DAT 88: M SAL 1 1 2 88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 0 0 0 0 0 0 0999 V2000 88: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 88: 1 2 1 0 88: M RGP 2 1 1 2 2 88: V 1 [*:1] 88: V 2 [*:2] 88: M END 88: 88: ******************************************** 88: $RXN 88: 88: RDKit 88: 88: 2 1 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 1 0 0 0 0 0 0999 V2000 88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 88: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 88: 1 2 1 0 88: V 1 halogen.bromine.aromatic 88: M STY 1 1 DAT 88: M SAL 1 1 1 88: M SED 1 [#35&$([Br&$(Br-&!@c)])] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 4 3 0 1 0 0 0 0 0 0999 V2000 88: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 2 3 1 0 88: 1 2 1 0 88: 2 4 1 0 88: V 2 boronicacid 88: M STY 1 1 DAT 88: M SAL 1 1 2 88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 0 0 0 0 0 0 0999 V2000 88: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 88: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 88: 1 2 1 0 88: M END 88: 88: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 88: $RXN 88: 88: RDKit 88: 88: 2 1 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 1 0 0 0 0 0 0999 V2000 88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 88: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 1 2 1 0 88: M RGP 1 2 1 88: V 1 halogen.bromine.aromatic 88: V 2 [*:1] 88: M STY 1 1 DAT 88: M SAL 1 1 1 88: M SED 1 [#35&$([Br&$(Br-&!@c)])] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 4 3 0 1 0 0 0 0 0 0999 V2000 88: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 2 3 1 0 88: 1 2 1 0 88: 2 4 1 0 88: M RGP 1 1 2 88: V 1 [*:2] 88: V 2 boronicacid 88: M STY 1 1 DAT 88: M SAL 1 1 2 88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 0 0 0 0 0 0 0999 V2000 88: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 88: 1 2 1 0 88: M RGP 2 1 1 2 2 88: V 1 [*:1] 88: V 2 [*:2] 88: M END 88: 88: ******************************************** 88: $RXN 88: 88: RDKit 88: 88: 2 1 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 1 0 0 0 0 0 0999 V2000 88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 88: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 88: 1 2 1 0 88: V 1 halogen.bromine.aromatic 88: M STY 1 1 DAT 88: M SAL 1 1 1 88: M SED 1 [#35&$([Br&$(Br-&!@c)])] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 4 3 0 1 0 0 0 0 0 0999 V2000 88: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 2 3 1 0 88: 1 2 1 0 88: 2 4 1 0 88: V 2 boronicacid 88: M STY 1 1 DAT 88: M SAL 1 1 2 88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 0 0 0 0 0 0 0999 V2000 88: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 88: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 88: 1 2 1 0 88: M END 88: [07:34:57] reactant 0 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] product 0 has no mapped atoms. 88: [07:34:57] Could not find RLabel mapping for atom: 0 in template: 1 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 88: [07:34:57] reactant 1 has no mapped atoms. 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: Atoms: 117: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 1 conj?: 1 aromatic?: 0 117: 1 1->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 12 conj?: 1 aromatic?: 1 117: 6 6->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 1 conj?: 1 aromatic?: 0 117: 9 8->10 order: 12 conj?: 1 aromatic?: 1 117: 10 10->1 order: 12 conj?: 1 aromatic?: 1 117: 11 7->3 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: SMI: Oc1cc2[nH]cnc2c(O)n1 117: Atoms: 117: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 105: [07:34:57] done 87: .[07:34:57] == testEnumerateLibrary 88: .. 88: ---------------------------------------------------------------------- 88: Ran 4 tests in 0.025s 88: 88: OK 88: 88: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 88: $RXN 88: 88: RDKit 88: 88: 2 1 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 1 0 0 0 0 0 0999 V2000 88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 88: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 1 2 1 0 88: M RGP 1 2 1 88: V 1 halogen.bromine.aromatic 88: V 2 [*:1] 88: M STY 1 1 DAT 88: M SAL 1 1 1 88: M SED 1 [#35&$([Br&$(Br-&!@c)])] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 4 3 0 1 0 0 0 0 0 0999 V2000 88: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 88: 2 3 1 0 88: 1 2 1 0 88: 2 4 1 0 88: V 2 boronicacid 88: M STY 1 1 DAT 88: M SAL 1 1 2 88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] 88: M END 88: $MOL 88: 88: RDKit 2D 88: 88: 2 1 0 0 0 0 0 0 0 0999 V2000 88: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 88: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 88: 1 2 1 0 88: M RGP 1 1 1 88: V 1 [*:1] 88: M END 88: 88: $RXN Failed 86: [07:34:57] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 78/223 Test #105: testPBF ................................ Passed 0.28 sec test 120 Start 120: fpTestCatch 120: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 120: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 120: Test timeout computed to be: 1500 117: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 1 conj?: 1 aromatic?: 0 117: 1 1->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 12 conj?: 1 aromatic?: 1 117: 6 6->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 1 conj?: 1 aromatic?: 0 117: 9 8->10 order: 12 conj?: 1 aromatic?: 1 117: 10 10->1 order: 12 conj?: 1 aromatic?: 1 117: 11 7->3 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: c1(O)cc2[nH]cnc2c(O)n1 117: Atoms: 117: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 1 conj?: 1 aromatic?: 0 117: 1 0->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 12 conj?: 1 aromatic?: 1 117: 6 6->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 1 conj?: 1 aromatic?: 0 117: 9 8->10 order: 12 conj?: 1 aromatic?: 1 117: 10 10->0 order: 12 conj?: 1 aromatic?: 1 117: 11 7->3 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: c1c(O)nc(O)c2c1[nH]cn2 117: Atoms: 117: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 12 conj?: 1 aromatic?: 1 117: 1 1->2 order: 1 conj?: 1 aromatic?: 0 117: 2 1->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 1 conj?: 1 aromatic?: 0 117: 5 4->6 order: 12 conj?: 1 aromatic?: 1 117: 6 6->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 12 conj?: 1 aromatic?: 1 117: 9 9->10 order: 12 conj?: 1 aromatic?: 1 117: 10 7->0 order: 12 conj?: 1 aromatic?: 1 117: 11 10->6 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: c12cc(O)nc(O)c1nc[nH]2 117: Atoms: 117: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 12 conj?: 1 aromatic?: 1 117: 1 1->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 1 conj?: 1 aromatic?: 0 117: 3 2->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 1 conj?: 1 aromatic?: 0 117: 6 5->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 12 conj?: 1 aromatic?: 1 117: 9 9->10 order: 12 conj?: 1 aromatic?: 1 117: 10 7->0 order: 12 conj?: 1 aromatic?: 1 117: 11 10->0 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: [nH]1c2cc(O)nc(O)c2nc1 117: Atoms: 117: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 79: [07:34:57] ------------------------------------- 79: [07:34:57] Testing matching E/Z against Cis/Trans stereo bonds 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: 200 104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 87: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> 87: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) 87: ResourceWarning: Enable tracemalloc to get the object allocation traceback 117: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 12 conj?: 1 aromatic?: 1 117: 1 1->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 1 conj?: 1 aromatic?: 0 117: 4 3->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 12 conj?: 1 aromatic?: 1 117: 6 6->7 order: 1 conj?: 1 aromatic?: 0 117: 7 6->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 12 conj?: 1 aromatic?: 1 117: 9 9->10 order: 12 conj?: 1 aromatic?: 1 117: 10 10->0 order: 12 conj?: 1 aromatic?: 1 117: 11 8->1 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: c1[nH]c2cc(O)nc(O)c2n1 117: Atoms: 117: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 12 conj?: 1 aromatic?: 1 117: 1 1->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 1 conj?: 1 aromatic?: 0 117: 5 4->6 order: 12 conj?: 1 aromatic?: 1 117: 6 6->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 1 conj?: 1 aromatic?: 0 117: 8 7->9 order: 12 conj?: 1 aromatic?: 1 117: 9 9->10 order: 12 conj?: 1 aromatic?: 1 117: 10 10->0 order: 12 conj?: 1 aromatic?: 1 117: 11 9->2 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: n1c[nH]c2cc(O)nc(O)c21 117: Atoms: 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 12 conj?: 1 aromatic?: 1 117: 1 1->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 1 conj?: 1 aromatic?: 0 79: [07:34:58] 79: 79: **** 79: Pre-condition Violation 79: matches must not be empty 79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 79: Failed Expression: !matches.empty() 79: **** 79: 117: 6 5->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 1 conj?: 1 aromatic?: 0 117: 9 8->10 order: 12 conj?: 1 aromatic?: 1 117: 10 10->0 order: 12 conj?: 1 aromatic?: 1 117: 11 10->3 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: c12c(cc(O)nc1O)[nH]cn2 117: Atoms: 117: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 12 conj?: 1 aromatic?: 1 117: 1 1->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 1 conj?: 1 aromatic?: 0 117: 4 3->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 12 conj?: 1 aromatic?: 1 117: 6 6->7 order: 1 conj?: 1 aromatic?: 0 117: 7 1->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 12 conj?: 1 aromatic?: 1 117: 9 9->10 order: 12 conj?: 1 aromatic?: 1 117: 10 6->0 order: 12 conj?: 1 aromatic?: 1 117: 11 10->0 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 117: Atoms: 117: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 1 conj?: 1 aromatic?: 0 117: 1 0->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 1 conj?: 1 aromatic?: 0 117: 6 5->7 order: 12 conj?: 1 aromatic?: 1 117: 7 3->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 12 conj?: 1 aromatic?: 1 117: 9 9->10 order: 12 conj?: 1 aromatic?: 1 117: 10 7->0 order: 12 conj?: 1 aromatic?: 1 117: 11 10->2 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: SMI: Oc1c2c(cc(O)n1)[nH]cn2 117: Atoms: 117: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 79: [07:34:58] 79: 79: **** 79: Pre-condition Violation 79: matches must not be empty 79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 79: Failed Expression: !matches.empty() 79: **** 79: 79: [07:34:58] ------------------------------------- 79: [07:34:58] Test substructure matching with a pathological case for symmetric SSSR 79: [07:34:58] ------------------------------------- 79: [07:34:58] Test isAtomTerminalRGroupOrQueryHydrogen 86: [07:34:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 86: .[07:34:58] 86: 86: **** 86: Pre-condition Violation 86: getNumImplicitHs() called without preceding call to calcImplicitValence() 86: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp 86: Failed Expression: d_implicitValence > -1 86: **** 86: 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 86: [07:34:58] 86: 86: **** 86: Pre-condition Violation 86: getNumImplicitHs() called without preceding call to calcImplicitValence() 86: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp 86: Failed Expression: d_implicitValence > -1 86: **** 86: 117: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: Bonds: 117: 0 0->1 order: 1 conj?: 1 aromatic?: 0 117: 1 1->2 order: 12 conj?: 1 aromatic?: 1 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 33: [07:34:58] Maximum BFS search size exceeded. 33: This is likely due to a highly symmetric fused ring system. 117: 5 5->6 order: 1 conj?: 1 aromatic?: 0 117: 6 5->7 order: 12 conj?: 1 aromatic?: 1 117: 7 3->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 12 conj?: 1 aromatic?: 1 117: 9 9->10 order: 12 conj?: 1 aromatic?: 1 117: 10 7->1 order: 12 conj?: 1 aromatic?: 1 117: 11 10->2 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test atom-pair fp generator 117: 117: SMI: n1c(O)cc2[nH]cnc2c1O 117: Atoms: 117: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: Bonds: 117: 0 0->1 order: 12 conj?: 1 aromatic?: 1 117: 1 1->2 order: 1 conj?: 1 aromatic?: 0 117: 2 1->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 12 conj?: 1 aromatic?: 1 117: 6 6->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 12 conj?: 1 aromatic?: 1 117: 9 9->10 order: 1 conj?: 1 aromatic?: 0 117: 10 9->0 order: 12 conj?: 1 aromatic?: 1 117: 11 8->4 order: 12 conj?: 1 aromatic?: 1 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 79/223 Test #79: testSubstructMatch ..................... Passed 0.45 sec test 121 Start 121: fpGenTestCatch 121: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 121: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 121: Test timeout computed to be: 1500 118: [07:34:58] done 118: [07:34:58] ------------------------------------- 118: [07:34:58] Test MHFP shingling creation 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 80/223 Test #92: pyTautomerQuery ........................ Passed 0.38 sec test 122 Start 122: pyTestGenerator 122: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 122: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 122: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: .......[07:34:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 86: [07:34:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 86: [07:34:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 86: [07:34:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 86: .[07:34:58] product atom-mapping number 1 found multiple times. 86: [07:34:58] product atom-mapping number 1 found multiple times. 27: ......[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 27: [07:34:58] 27: 27: **** 27: Invariant Violation 27: bad direction in linearSearch 27: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h 27: Failed Expression: status >= 0 27: **** 27: 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test atom-pair fp generator with different arguments 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation 109: [07:34:58] done 109: [07:34:58] ------------------------------------- 109: [07:34:58] More PMI/NPR tests. 109: [07:34:58] done 109: [07:34:58] ------------------------------------- 109: [07:34:58] Basic NPR tests. 82: [07:34:58] reactant 0 has no mapped atoms. 82: [07:34:58] product 0 has no mapped atoms. 82: [07:34:58] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. 81: Randomness seeded to: 3379151290 81: =============================================================================== 81: All tests passed (9408 assertions in 38 test cases) 81: 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Morgan Fingerprints. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Morgan Fingerprints using fromAtoms argument. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Morgan Fingerprints as bit vects. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Morgan Fingerprints with feature invariants. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test additional Morgan fingerprints options. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Atom Codes. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Atom Pairs. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Atom Pairs part 2. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Topological Torsions. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Bulk Topological Torsions. 81/223 Test #81: testGenericGroups ...................... Passed 0.43 sec test 123 Start 123: pyTestMHFP 123: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 123: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 123: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: ................[07:34:58] mapped atoms in the reactants were not mapped in the products. 86: unmapped numbers are: 3 86: [07:34:58] mapped atoms in the reactants were not mapped in the products. 86: unmapped numbers are: 3 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test atom-pair additional output 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Folded Atom Pairs. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Rooted Atom Pairs. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test ignoring atoms in Atom Pairs. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Atom Pairs including info about chirality. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Morgan Fingerprints. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test morgan fp generator 99: ......... 99: ---------------------------------------------------------------------- 99: Ran 9 tests in 0.063s 99: 99: OK 82/223 Test #82: testReaction ........................... Passed 0.43 sec test 124 Start 124: testPartialCharges 124: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 124: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges 124: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: .[07:34:58] mapped atoms in the reactants were not mapped in the products. 86: unmapped numbers are: 3 118: [07:34:58] done 118: [07:34:58] ------------------------------------- 118: [07:34:58] Test MHFP hashing of string and uint arrays 118: [07:34:58] done 118: [07:34:58] ------------------------------------- 118: [07:34:58] Test SECFP fingerprint functionality 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: ..[07:34:58] reactant 2 has no mapped atoms. 86: [07:34:58] reactant 2 has no mapped atoms. 86: [07:34:58] product 1 has no mapped atoms. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 87: ..[07:34:58] == testRGroupState 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Morgan Fingerprints using fromAtoms argument. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Morgan Fingerprints as bit vects. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Morgan Fingerprints with feature invariants. 118: [07:34:58] done 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test additional Morgan fingerprints options. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 83/223 Test #118: testMHFPFingerprint .................... Passed 0.08 sec test 125 Start 125: pyPartialCharges 125: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 125: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 125: Test timeout computed to be: 1500 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Single atoms setting radius 1 bits in Morgan fingerprints 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test different invariant generator combinations 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test invariant overriding 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test RDKit fp generator 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 87: .[07:34:58] == testRandomEnumerateAllBBsLibrary 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: ........[07:34:58] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q 86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' 86: [07:34:58] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q 86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 87: ** [1, 1] 87: ** [0, 2] 87: ** [1, 0] 86: .[07:34:58] reactant atom-mapping number 1 found multiple times. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: [07:34:58] product atom-mapping number 2 not found in reactants. 120: Randomness seeded to: 1986149471 120: =============================================================================== 120: All tests passed (166 assertions in 14 test cases) 120: 86: [07:34:58] mapped atoms in the reactants were not mapped in the products. 86: unmapped numbers are: 4 86: [07:34:58] product atom-mapping number 5 not found in reactants. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 84/223 Test #120: fpTestCatch ............................ Passed 0.07 sec 85/223 Test #124: testPartialCharges ..................... Passed 0.03 sec test 126 Start 126: testMolTransforms 126: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 126: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 126: Test timeout computed to be: 1500 test 127 Start 127: pyMolTransforms 127: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 127: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 127: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 87: .[07:34:58] == testRandomEnumerateLibrary 86/223 Test #88: pyChemReactionSanitize ................. Passed 0.45 sec test 128 Start 128: testMMFFForceFieldHelpers 128: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 128: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 128: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 87: .[07:34:58] == testRandomSample 62: ..............[07:34:58] SMILES Parse Error: syntax error while parsing: invalidsmiles 62: [07:34:58] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 87: .[07:34:58] == testRandomSampleAllBBs 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 101: [07:34:58] done 87/223 Test #99: pyFragCatalog .......................... Passed 0.43 sec test 129 Start 129: testMMFFForceFieldHelpersMultiThread 129: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 129: Test timeout computed to be: 1500 101: [07:34:58] ------------------------------------- 101: [07:34:58] Test Github #3806: NaNs from AUTOCORR2D descriptor 101: [07:34:58] done 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] ------------------------------------- 128: [07:34:58] Test MMFF atom types. 88/223 Test #101: testAUTOCORR2D ......................... Passed 0.42 sec test 130 Start 130: testUFFForceFieldHelpers 130: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 130: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 130: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: ........./build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> 86: png = open(fname, 'rb').read() 86: ResourceWarning: Enable tracemalloc to get the object allocation traceback 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 34 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 36 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 38 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 40 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 42 87: .[07:34:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 87: [07:34:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 87: .[07:34:58] == testRemoveBadMatches 87: .[07:34:58] == testTimings 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 87 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 89 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 91 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 93 86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 95 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing MMFF builder tools. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 126: *********************************************************** 126: Testing MolTransforms 126: --------------------------------- 126: test1Canonicalization 126: 126: --------------------------------- 126: testGetSetBondLength 126: 126: --------------------------------- 126: testGetSetAngle 126: 126: --------------------------------- 126: testGetSetDihedral 126: 126: --------------------------------- 126: testGetSetDihedralThroughTripleBond 126: 126: --------------------------------- 126: testGithub1262: PMI descriptors incorrect 126: 126: --------------------------------- 126: testGithub1908: CanonicalizeMol() distorting bond lengths 126: 126: --------------------------------- 126: testGithub4302: native computeCanonicalTransform() generates non-canonical coords 126: 126: --------------------------------- 126: testWeightedCentroid 126: 126: *********************************************************** 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 89/223 Test #126: testMolTransforms ...................... Passed 0.06 sec test 131 Start 131: testCrystalForceField 131: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 131: Test timeout computed to be: 1500 86: ..[07:34:58] SMARTS Parse Error: syntax error while parsing: boromicacid 86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 130: [07:34:58] ------------------------------------- 130: [07:34:58] Test UFF atom labels. 129: [07:34:58] ------------------------------------- 129: [07:34:58] Test MMFF multithreading 86: [07:34:58] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 86: [07:34:58] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 86: [07:34:58] reaction has no reactants 86: [07:34:58] reaction has no products 86: [07:34:58] initialization failed 86: [07:34:58] reaction has no reactants 86: [07:34:58] reaction has no products 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing MMFF builder+minimization. 104: 300 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 131: ------------------------------------- 131: Test CrystalFF torsional term. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Test UFF atom typer. 86: .[07:34:58] SMARTS Parse Error: syntax error while parsing: boromicacid 86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: [07:34:58] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 86: [07:34:58] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: [07:34:58] reaction has no reactants 86: [07:34:58] reaction has no products 86: [07:34:58] initialization failed 86: [07:34:58] reaction has no reactants 86: [07:34:58] reaction has no products 86: . 86: ---------------------------------------------------------------------- 86: Ran 50 tests in 0.157s 86: 86: OK 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 86: ******************************************** 86: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn 86: 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing UFF builder tools. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing UFF builder+minimization. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 110: =>start test WHIM 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 110: [07:34:58] test on : 365 molecules done 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 90/223 Test #110: testWHIM ............................... Passed 0.40 sec test 132 Start 132: pyForceFieldHelpers 132: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 132: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 132: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 4: dynamic RDAny:0.37222 s 4: static RDValue:1e-06 s 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing Issue239. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Hashed Atom Pairs. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Hashed torsions. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Rooted Atom Pairs. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test ignoring atoms in Atom Pairs. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Rooted Topological Torsions. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test ignoring atoms in Topological Torsions. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test atom info from morgan fingerprints. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: [07:34:58] Test atom info from morgan fingerprints including Info Redundant Environments. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] ------------------------------------- 129: processing 129: launch :0 117: [07:34:58] ------------------------------------- 129: launch :1 129: launch :2 129: launch :3 129: launch :4 129: launch :5 129: launch :6 129: launch :7 129: launch :8 129: launch :9 129: launch :10 129: launch :11 129: launch :12 129: launch :13 129: launch :14 129: launch :15 129: launch :16 129: launch :17 129: launch :18 129: launch :19 129: launch :20 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 129: launch :21 129: launch :22 129: launch :23 62: ..... 62: ---------------------------------------------------------------------- 62: Ran 19 tests in 0.421s 62: 62: OK 121: Randomness seeded to: 755712616 121: =============================================================================== 121: All tests passed (2678 assertions in 4 test cases) 121: 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: [07:34:58] ------------------------------------- 117: [07:34:58] ------------------------------------- 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Atom Pairs including info about chirality. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test Topological Torsions including info about chirality. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test GitHub Issue 25: fingerprint backwards compatibility. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test GitHub Issue 151: PatternFingerprint problems 91/223 Test #121: fpGenTestCatch ......................... Passed 0.21 sec test 133 Start 133: testDistGeomHelpers 133: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 133: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 133: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing calcEnergy with passed coords. 92/223 Test #86: pyChemReactions ........................ Passed 0.61 sec test 134 Start 134: distGeomHelpersCatch 134: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 134: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 134: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test 3D atom pairs. 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule 117: [07:34:58] done 117: [07:34:58] ------------------------------------- 117: [07:34:58] Test multithreading with the pattern FP 117: reading molecules 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing calcGrad. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 109: [07:34:58] done 109: [07:34:58] ------------------------------------- 109: [07:34:58] PMI edge cases. 109: [07:34:58] done 109: [07:34:58] ------------------------------------- 109: [07:34:58] NPR edge cases. 109: [07:34:58] done 109: [07:34:58] ------------------------------------- 109: [07:34:58] 3D descriptors. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 109: [07:34:58] done 109: [07:34:58] ------------------------------------- 109: [07:34:58] 3D descriptor edge cases. 109: [07:34:58] done 109: [07:34:58] ------------------------------------- 109: [07:34:58] Inertial shape factor. 109: [07:34:58] done 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 93/223 Test #109: test3D ................................. Passed 0.51 sec test 135 Start 135: pyDistGeomHelpers 135: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 135: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 135: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: pass 1 117: launch :0 117: launch :1 117: launch :2 117: launch :3 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 106: =>start test rdf custom 106: [07:34:58] test on : 365 molecules done 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 56: Randomness seeded to: 3731930439 56: =============================================================================== 56: All tests passed (1902 assertions in 21 test cases) 56: 134: Randomness seeded to: 367100113 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing Issue242. 94/223 Test #56: cxsmilesTest ........................... Passed 0.81 sec test 136 Start 136: testMolAlign 136: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 136: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 136: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 27: ... 27: ---------------------------------------------------------------------- 27: Ran 12 tests in 0.613s 27: 27: OK 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing UFF special cases. 130: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 0 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing Issue239. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 4: dynamic RDValue:0.065841 s 4: deleted! 4: [07:34:58] ------------------------------------- 4: [07:34:58] Testing String Pickle Roundtrips. 4: [07:34:58] done 4: [07:34:58] ------------------------------------- 4: [07:34:58] Testing conversion of vect to string. 4: [07:34:58] done 4: [07:34:58] ------------------------------------- 4: [07:34:58] Testing returning const references. 4: [07:34:58] any cast 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 133: go 4: [07:34:58] done: 0.001349 300000 4: [07:34:58] copy 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 4: [07:34:58] done: 0.001283 300000 4: [07:34:58] ref 133: ------------------------------------- 133: 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 4: [07:34:58] done: 0.001275 300000 4: [07:34:58] dict 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 4: [07:34:58] done: 0.00304 300000 4: [07:34:58] ref with hasVal 104: 400 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 4: [07:34:58] done: 0.001966 300000 4: [07:34:58] done 4: [07:34:58] ------------------------------------- 4: [07:34:58] Testing dict update. 4: [07:34:58] done 4: deleted! 4: deleted! 4: deleted! 4: deleted! 4: deleted! 4: deleted! 95/223 Test #4: testDict ............................... Passed 0.95 sec test 137 Start 137: testO3AAlign 137: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 137: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 137: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing calcEnergy with passed coords. 112: =>start test autocorr3D 112: [07:34:58] test on : 365 molecules done 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing github 308: crash during MMFF parameterization . 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 96/223 Test #62: pyDepictor ............................. Passed 0.82 sec test 138 Start 138: molAlignCatchTest 138: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 138: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 138: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [07:34:58] ------------------------------------- 103: [07:34:58] Test empty molecule BCUT. 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing SFIssue1653802. 97/223 Test #112: testAUTOCORR3D ......................... Passed 0.45 sec test 139 Start 139: pyMolAlign 139: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 139: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 139: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Testing SFIssue2378119. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing calcGrad. 98/223 Test #103: testBCUT ............................... Passed 0.61 sec test 140 Start 140: testFeatures 140: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 140: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures 140: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: [07:34:58] done 128: [07:34:58] ------------------------------------- 128: [07:34:58] Test MMFF force-field parameter getters. 128: [07:34:58] ------------------------------------- 128: [07:34:58] Test MMFF multithreading 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 99/223 Test #131: testCrystalForceField .................. Passed 0.19 sec test 141 Start 141: pyChemicalFeatures 141: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 141: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 141: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing SFIssue1653802. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing SFIssue2378119. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Test UFF force-field parameter getters. 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing handling missing parameters. 130: [07:34:58] UFFTYPER: Unrecognized hybridization for atom: 0 130: [07:34:58] UFFTYPER: Unrecognized atom type: Cu+1 (0) 130: [07:34:58] UFFTYPER: Unrecognized hybridization for atom: 0 130: [07:34:58] UFFTYPER: Unrecognized atom type: Cu+1 (0) 140: [07:34:58] ------------------------------------- 140: [07:34:58] AtomType parser testing. 140: [07:34:58] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] 140: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] FeatureDefinition parser testing. 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Test pulling feat defs from a string. 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] FeatureDef functionality testing. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: generating reference data 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Testing SFIssue3009337. 130: [07:34:58] done 130: [07:34:58] ------------------------------------- 130: [07:34:58] Test UFF multithreading 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] FeatureFactory testing. 140: [07:34:58] 1 140: [07:34:58] 2 140: [07:34:58] 3 140: [07:34:58] 4 140: [07:34:58] 5 140: [07:34:58] 6 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Feature Location testing. 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Test building a FeatureFactory from a file 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Testing Issue 224. 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Testing Issue 225. 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Test Issue346 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Test Issue347 140: [07:34:58] done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Testing Issue 348. 140: [07:34:58] SMARTS Parse Error: syntax error while parsing: [C[C] 140: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' 140: [07:34:58] ------------------------------------- 140: [07:34:58] Testing Nested AtomType definitions. 140: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] 140: [07:34:58] ------------------------------------- 140: [07:34:58] Testing Github Issue #252: crash when calling getPos() with no conformer. 140: [07:34:58] expect a precondition failure message below 140: [07:34:58] 140: 140: **** 140: Pre-condition Violation 140: molecule has no conformers 140: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 140: Failed Expression: dp_mol->getNumConformers() 140: **** 140: 140: [07:34:58] Done 140: [07:34:58] ------------------------------------- 140: [07:34:58] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() 140: [07:34:58] done 100/223 Test #140: testFeatures ........................... Passed 0.03 sec test 142 Start 142: testShapeHelpers 142: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 142: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 142: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 130: generating reference data 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 134: [07:34:58] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test unfolded version of RDKFP 134: [07:34:58] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test topological torsion fp generator 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 134: [07:34:58] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] 107: =>start test rdf 107: [07:34:58] test on : 365 molecules done 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 134: [07:34:58] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Topological Torsions. 101/223 Test #107: testRDF ................................ Passed 0.66 sec test 143 Start 143: pyShapeHelpers 143: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 143: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 143: Test timeout computed to be: 1500 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Folded torsions. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Bulk Topological Torsions. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 134: [07:34:58] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 123: .. 123: ---------------------------------------------------------------------- 123: Ran 2 tests in 0.035s 123: 123: OK 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 134: [07:34:58] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 134: [07:34:58] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 142: *********************************************************** 142: Testing ShapeHelpers 142: --------------------------------- 142: test1Encode 142: 142: --------------------------------- 142: test2Compare 142: 142: --------------------------------- 142: testGithub4364 142: 142: *********************************************************** 102/223 Test #27: pyForceFieldConstraints ................ Passed 1.03 sec 103/223 Test #142: testShapeHelpers ....................... Passed 0.07 sec test 144 Start 144: testMolCatalog 144: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 144: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 144: Test timeout computed to be: 1500 test 145 Start 145: pyMolCatalog 145: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 145: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 145: Test timeout computed to be: 1500 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: Elapsed time: 0.676973 s 104: Errors:0 104: [07:34:58] test on : 500 molecules done 134: [07:34:58] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 134: [07:34:58] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: ----------- 115: .....[07:34:58] 115: 115: **** 115: Pre-condition Violation 115: Number of atom props not equal to number of atoms 115: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp 115: Failed Expression: atom_props.size() == num_atoms 115: **** 115: 136: *********************************************************** 136: Testing MolAlign 136: --------------------------------- 136: test1MolAlign 136: 136: --------------------------------- 136: test1GetBestRMS 136: 136: --------------------------------- 136: test1MolWithQueryAlign 136: 136: --------------------------------- 136: test2AtomMap 136: 136: --------------------------------- 136: test3Weights 136: 136: --------------------------------- 136: testIssue241 136: 136: *********************************************************** 104/223 Test #104: testEEM ................................ Passed 0.71 sec 105/223 Test #136: testMolAlign ........................... Passed 0.15 sec test 146 Start 146: moldraw2DTest1 146: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 146: Test timeout computed to be: 1500 test 147 Start 147: moldraw2DTestCatch 147: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 147: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 147: Test timeout computed to be: 1500 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 134: ----------- 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [07:34:58] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 106/223 Test #144: testMolCatalog ......................... Passed 0.04 sec test 148 Start 148: moldraw2DRxnTest1 148: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 148: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 148: Test timeout computed to be: 1500 134: ----------- 107/223 Test #123: pyTestMHFP ............................. Passed 0.41 sec test 149 Start 149: pyMolDraw2D 149: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 149: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 149: Test timeout computed to be: 1500 129: done 98: [07:34:58] 98: 98: **** 98: Invariant Violation 98: nonsense 98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 98: Failed Expression: token != tokens.end() 98: **** 98: 98: [07:34:58] 98: 98: **** 115: ......................... 115: ---------------------------------------------------------------------- 115: Ran 30 tests in 0.054s 115: 98: Invariant Violation 98: nonsense no new line 98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 98: Failed Expression: token != tokens.end() 98: **** 98: 98: [07:34:58] 98: 98: **** 98: Invariant Violation 98: nonsense with tab 98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 98: Failed Expression: token != tokens.end() 98: **** 98: 115: OK 115: exactmw 78.046950192 115: amw 78.11399999999999 115: lipinskiHBA 0.0 115: lipinskiHBD 0.0 115: NumRotatableBonds 0.0 115: NumHBD 0.0 115: NumHBA 0.0 115: NumHeavyAtoms 6.0 115: NumAtoms 6.0 115: NumHeteroatoms 0.0 115: NumAmideBonds 0.0 115: FractionCSP3 0.0 115: NumRings 1.0 115: NumAromaticRings 1.0 115: NumAliphaticRings 0.0 115: NumSaturatedRings 0.0 115: NumHeterocycles 0.0 115: NumAromaticHeterocycles 0.0 115: NumSaturatedHeterocycles 0.0 115: NumAliphaticHeterocycles 0.0 115: NumSpiroAtoms 0.0 115: NumBridgeheadAtoms 0.0 115: NumAtomStereoCenters 0.0 115: NumUnspecifiedAtomStereoCenters 0.0 115: labuteASA 37.43140311949697 115: tpsa 0.0 115: CrippenClogP 1.6866 115: CrippenMR 26.441999999999993 115: chi0v 3.464101615137755 115: chi1v 2.0000000000000004 115: chi2v 0.6666666666666671 115: chi3v 0.6666666666666671 115: chi4v 0.38490017945975075 115: chi0n 3.464101615137755 115: chi1n 2.0000000000000004 115: chi2n 0.6666666666666671 115: chi3n 0.6666666666666671 115: chi4n 0.38490017945975075 115: hallKierAlpha -0.78 115: kappa1 3.4115708812260532 115: kappa2 1.6057694396735218 115: kappa3 0.5823992601400448 115: Phi 0.9130327103921437 115: exactmw 78.046950192 115: lipinskiHBA 0.0 134: ----------- 108/223 Test #98: testFragCatalog ........................ Passed 0.78 sec test 150 Start 150: testFMCS 150: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 150: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 150: Test timeout computed to be: 1500 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [07:34:58] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 138: Randomness seeded to: 118416601 138: 112543012 146: ----------------- Test 1 134: [07:34:58] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [07:34:58] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 129: [07:34:58] done 148: ----------------- Test 1 127: ........ 127: ---------------------------------------------------------------------- 127: Ran 8 tests in 0.034s 127: 127: OK 147: Randomness seeded to: 2597391031 147: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U 146: file test1_5.svg gave hash 2383324771U not the expected 2811480876U 146: Done 146: ----------------- Test 2 109/223 Test #129: testMMFFForceFieldHelpersMultiThread ... Passed 0.41 sec test 151 Start 151: pyFMCS 151: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" 151: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 151: Test timeout computed to be: 1500 146: file test2_1.png gave hash 1188732611U not the expected 307437906U 148: file rxn_test1_1.png gave hash 1121707892U not the expected 1556334749U 110/223 Test #115: pyMolDescriptors ....................... Passed 0.61 sec test 152 Start 152: FMCStest 152: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 152: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 152: Test timeout computed to be: 1500 146: file test2_2.png gave hash 206445131U not the expected 610424244U 122: ............. 122: ---------------------------------------------------------------------- 122: Ran 13 tests in 0.181s 122: 122: OK 117: pass 2 117: launch :0 117: launch :1 117: launch :2 117: launch :3 147: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Rooted Topological Torsions. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test ignoring atoms in Topological Torsions. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test Topological Torsions including info about chirality. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test GitHub Issue 25: fingerprint backwards compatibility. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 111/223 Test #127: pyMolTransforms ........................ Passed 0.46 sec test 153 Start 153: molHashCatchTest 153: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 153: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash 153: Test timeout computed to be: 1500 64: [07:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [07:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [07:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [07:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [07:34:58] deprecated group abbreviation ignored on line 24 64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 64: [07:34:58] 64: 64: **** 64: Post-condition Violation 64: Element 'Mv' not found 64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 64: Failed Expression: anum > -1 64: **** 64: 147: file contourMol_2.svg gave hash 2850811663U not the expected 572669511U 146: Done 146: ----------------- Test 4 119: [07:34:58] done 119: [07:34:58] ------------------------------------- 119: [07:34:58] Test convenience and bulk fp calculation functions 116: ........ 116: ---------------------------------------------------------------------- 116: Ran 8 tests in 0.205s 116: 116: OK 148: file rxn_test1_2.png gave hash 1557885590U not the expected 1924084263U 138: 84897061 33: [07:34:58] Maximum BFS search size exceeded. 33: This is likely due to a highly symmetric fused ring system. 146: file test4_1.png gave hash 297807158U not the expected 1403972924U 146: Done 146: ----------------- Test 5 147: file contourMol_3.svg gave hash 1894450507U not the expected 936771429U 147: file contourMol_4.svg gave hash 1717526955U not the expected 3302971362U 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_15113.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_16613.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_30745.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_30861.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_31495.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_34869.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_36158.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_36559.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_37434.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_39147.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_43754.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_44011.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_44158.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_48076.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_48961.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_49648.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_49703.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_51128.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_51343.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_51842.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_54554.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_100_55749.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_17256.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20244.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20245.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30149.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30499.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_36186.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_39262.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_43966.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_45279.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_48029.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49064.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49801.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_50681.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_54039.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58265.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58358.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58866.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10188_60810.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21358.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21597.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30111.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30349.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31746.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31822.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_35220.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37603.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37964.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_39508.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42164.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42577.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_44072.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_45522.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46700.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46719.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46744.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_48517.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_49087.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_50034.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_51475.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53483.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53506.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_54598.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55614.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55737.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57090.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57705.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57785.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_58463.txt 152: 152: testChEMBfopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: L_Txt() chembl_II_sets/Target_no_10193_58700.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61003.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61349.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10260_38526.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10260_50778.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10260_52179.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10260_54285.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_30224.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_31222.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37349.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37369.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37465.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37541.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_38371.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44314.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44578.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_45765.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_46281.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_47928.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_50624.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51341.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51662.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51767.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53081.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53396.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53407.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_58823.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_59190.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_60672.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10280_61176.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10434_20905.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30074.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30175.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30423.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10434_31555.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10434_34878.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10434_35926.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10434_42168.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_20859.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_30060.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_30061.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_30606.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_30866.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_31249.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_34921.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_35188.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_36636.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_37466.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_39202.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_43952.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_49345.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_49591.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_49854.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_51416.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_53537.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_58879.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_60679.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_107_61269.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_20600.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_20859.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_30060.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_30606.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_30866.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_31558.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_35188.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_37466.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_43875.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_48911.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_49591.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_49854.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: no_108_57887.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_60679.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_108_6857.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_15478.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_20853.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30840.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30862.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30918.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30994.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31014.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31508.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31623.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35003.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35004.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35281.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35957.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36520.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36641.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_38586.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_44431.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_45093.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_51302.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5247.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_52937.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_57198.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5739.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_10980_6535.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20205.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20986.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_30091.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34698.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34705.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37038.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37272.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37447.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38909.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38953.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_39472.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_45825.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_47179.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49028.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49860.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_51984.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53395.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53826.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54121.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54530.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_55738.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_57725.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11140_58590.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11365_20432.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11365_30331.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11365_37956.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11365_48114.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11365_58566.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34731.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34818.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37318.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37339.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37564.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39504.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39561.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46082.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46089.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47349.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47757.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_51593.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_54754.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58262.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58958.txt 152: 152: testChEMBL_Txt(fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: ) chembl_II_sets/Target_no_114_16827.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_20503.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_20724.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_30254.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_30321.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_30572.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_31116.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_31281.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_31443.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_34747.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_34920.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_35040.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_36623.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_37136.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_37208.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_38298.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_38554.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_39088.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_39543.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_44049.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_44562.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_45180.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_45867.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_46087.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_46829.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_47546.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_48395.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_50461.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_50765.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_51669.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_52381.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_57231.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_114_58246.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_30999.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31021.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31650.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_35011.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_37014.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_44598.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_48446.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50614.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50615.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50618.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11534_51950.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11575_31616.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11575_38381.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11575_45757.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11575_46816.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11575_50701.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11575_54049.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11575_57890.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11575_61045.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11631_30194.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11631_31421.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11631_35538.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11631_55727.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11631_60676.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11631_61130.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_11631_6444.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_15623.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_20096.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_21591.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_30184.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_30380.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_30745.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_30861.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_31619.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_34869.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_35284.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_36158.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_36915.txt 152: 152: testChEMBL_Txfopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: t() chembl_II_sets/Target_no_121_37434.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_37541.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_37677.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_38837.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_39530.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_43793.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_44158.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_44164.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_44579.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_44593.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_44692.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_44914.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_45878.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_48050.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_48706.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_48944.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_48961.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_49880.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_50055.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_50512.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_51064.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_53537.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_55749.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_58879.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_121_6876.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12209_44664.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12209_46451.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12209_50640.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12209_56102.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12209_58015.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59089.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59092.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12209_61340.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12252_31458.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12252_38481.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12252_42104.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49475.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49933.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12252_50558.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_126_37249.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_126_39117.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_126_48227.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_126_48229.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_126_53969.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_126_54262.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_126_55353.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_126_61212.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20250.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20506.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20626.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20689.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_21358.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30158.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30349.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_34843.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_35220.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36318.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36800.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_39349.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45385.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45676.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46700.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46719.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_48517.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_52690.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_53483.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_55435.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_56102.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58015.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58375.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_1295fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: 2_58700.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_16724.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_2710.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_30128.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_31250.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_35519.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_36905.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_46788.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_4737.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_55736.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_13001_57473.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_16146.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_30313.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_30539.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_30653.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_30988.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_31179.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_31339.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_3525.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_36886.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_37020.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_38128.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_43952.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_45210.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_45899.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_47889.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_51800.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_53158.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_5330.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_55648.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_56096.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_57287.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_57399.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_57606.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_58470.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_130_60894.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_15010.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_20304.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_20542.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_20788.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_21358.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_30349.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_31103.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_31764.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_31822.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_35220.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_37964.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_42164.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_44072.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_45522.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_46719.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_46744.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_48416.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_49740.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_50034.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_50640.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_53483.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_53506.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_53814.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_55435.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_56074.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_56107.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_57090.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_57705.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_57785.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_57861.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_58583.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_59089.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_15_59092.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_20600.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_30764.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_34876.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_37427.tfopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: xt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_38266.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_45283.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_46990.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_47123.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_47900.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_48050.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_48062.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_48076.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_50718.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_50972.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_51372.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_51830.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_53049.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_53505.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_54021.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_54565.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_54570.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_57666.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_57890.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_58072.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_58634.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_58643.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_59080.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_59202.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_59346.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_60379.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_60385.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_165_61098.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_17045_31154.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_17045_35648.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_17045_48914.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_17045_51975.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_17045_52435.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_17045_55790.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_17045_58958.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_17045_61146.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20191.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20562.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20606.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20607.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30003.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30402.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30726.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30924.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31457.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31460.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31600.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31620.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31640.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31782.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31797.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31829.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31856.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34690.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34691.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34694.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_35712.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37497.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37539.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48070.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48219.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48824.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48902.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_52867.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_53534.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_54570.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_58727.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60159.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60661.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_30037.txt 152: 152: testChEMBL_Txt() chefopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: mbl_II_sets/Target_no_259_34734.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_35365.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_35787.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_36793.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_37845.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_38328.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_39374.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_43936.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_44059.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_44405.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_44424.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_45166.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_46158.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_46425.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_47187.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_48435.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_48817.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_48849.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_48957.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_48965.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_49519.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_49921.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_50392.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_50972.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_52405.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_52442.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_53169.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_54640.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_57207.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_58537.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_58920.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_259_60358.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_25_16077.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_25_34943.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_25_36391.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_25_36574.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_25_52906.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_25_54642.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_16385.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_20333.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_20774.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_35825.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_37637.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_47741.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_48567.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_48841.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_49589.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_50564.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_51201.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_53150.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_55747.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_43_58276.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_20813.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_2331.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_2391.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_30374.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_30512.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_30796.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_31058.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_31450.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_36609.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_36636.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_38266.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_43800.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_47621.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_49433.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_49550.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_49865.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_51005.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_52373.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_53878.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 147: file contourMol_5.svg gave hash 1093404576U not the expected 2230414999U 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_57618.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_59484.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_51_6563.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_61_16845.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_61_37106.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_61_37272.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_61_47947.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_61_50754.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_61_55800.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_61_57380.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_65_35328.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_65_36137.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_65_38826.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_65_44596.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_65_51275.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_65_55671.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_20155.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_30616.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_30653.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_30988.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_31339.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_31527.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_31631.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_36047.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_36568.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_36636.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_37020.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_38128.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_43952.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_45210.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_47889.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_51064.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_51800.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_5330.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_57508.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_58470.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_72_60894.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_20730.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_20753.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_30097.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_30663.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_35365.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_35375.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_35918.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_36010.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_36780.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_36793.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_37845.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_39110.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_39546.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_43936.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_44405.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_44424.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_44683.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_45166.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_46648.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_46986.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_47070.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_47187.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_48435.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_48817.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_49138.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_49460.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_49519.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_49532.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_49829.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_50608.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_54640.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_87_61082.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_90_15727.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_90_20155.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_90_30407.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_90_3525.txt 152: 152: testChEMBfopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: L_Txt() chembl_II_sets/Target_no_93_12377.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_93_1308.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_93_34759.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_93_35447.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_93_42214.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_93_45877.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_93_47082.txt 152: 152: testChEMBL_Txt() chembl_II_sets/Target_no_93_57082.txt 152: 152: testFileSDF_RandomSet(): benchmark/chembl13-10000-random-pairs.sdf 152: ERROR: RDKit could not load input file 152: 152: testFileSDF_RandomSet(): benchmark/chembl13_pairs.smi 152: ERROR: RDKit could not load input file 152: 152: testFileSDF_RandomSet(): benchmark/chembl13_knearest_2.smi 152: ERROR: RDKit could not load input file 152: 152: testFileSDF_RandomSet(): benchmark/chembl13_knearest_10.smi 152: ERROR: RDKit could not load input file 152: 152: testFileSDF_RandomSet(): benchmark/chembl13_knearest_100.smi 152: ERROR: RDKit could not load input file 152: 152: testFileSDF_RandomSet(): benchmark/chembl13_threshold_80.smi 152: ERROR: RDKit could not load input file 152: 152: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 152: ERROR: RDKit could not load input file 146: file test5_1.png gave hash 1384886438U not the expected 1269428339U 148: file rxn_test1_3.png gave hash 3006127285U not the expected 1644921059U 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 112/223 Test #152: FMCStest ............................... Passed 0.05 sec test 154 Start 154: pyMolHash 154: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 154: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 154: Test timeout computed to be: 1500 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 146: file test5_2.png gave hash 3891642937U not the expected 3073694291U 148: file rxn_test1_4.png gave hash 326223573U not the expected 2471435686U 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 146: file test5_3.png gave hash 442326768U not the expected 1865192682U 146: Done 146: ----------------- Test 6 (atom labels) 134: [07:34:58] UFFTYPER: Unrecognized atom type: Pt5+2 (1) 134: [07:34:58] UFFTYPER: Unrecognized atom type: N_5 (2) 134: [07:34:58] UFFTYPER: Unrecognized atom type: N_5 (3) 134: [07:34:58] UFFTYPER: Unrecognized atom type: N_5 (2) 134: [07:34:58] UFFTYPER: Unrecognized atom type: N_5 (3) 146: Done 146: ----------------- Test 7 (backgrounds) 148: file rxn_test1_5.png gave hash 1915733777U not the expected 1428782307U 33: F/C=C/Cl 33: [H]/C(F)=C(/[H])Cl 33: F/C=C/Cl 33: F/C=C/Cl 33: C/C(F)=C(/C)Cl 147: file testGithub3226_1.png gave hash 1140467476U not the expected 2350054896U 146: file test7_1.png gave hash 2325902062U not the expected 3033050306U 113/223 Test #116: pyMolDescriptors3D ..................... Passed 0.67 sec test 155 Start 155: testMMPA 155: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 155: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 155: Test timeout computed to be: 1500 134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 1 147: file testGithub3226_2.png gave hash 1788850357U not the expected 606206725U 146: file test7_2.png gave hash 3963123595U not the expected 3476380724U 146: Done 146: ----------------- Test8: PrepareMolDrawing 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 146: Done 146: ----------------- Test multi-threaded drawing 146: reading molecules 134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 1 130: processing 130: launch :0 130: launch :1 130: launch :2 130: launch :3 114/223 Test #122: pyTestGenerator ........................ Passed 0.60 sec test 156 Start 156: pyMMPA 156: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" 156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap 156: Test timeout computed to be: 1500 130: [07:34:58] Rep: 0 Mol:2 130: [07:34:58] Rep: [07:34:58] Rep: 00 Mol:3 130: Mol:1 130: [07:34:58] Rep: 0 Mol:5 153: Randomness seeded to: 2552094542 153: =============================================================================== 153: All tests passed (304 assertions in 9 test cases) 153: 148: file rxn_test1_6.png gave hash 793678174U not the expected 483353696U 147: file testGithub3226_3.png gave hash 2180602679U not the expected 2282880418U 115/223 Test #153: molHashCatchTest ....................... Passed 0.09 sec test 157 Start 157: testRascalMCES 157: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES 157: Test timeout computed to be: 1500 130: [07:34:58] Rep: 0 Mol:0 130: [07:34:58] Rep: 0 Mol:9 147: file testPNGMetadata_1.png gave hash 3955478692U not the expected 2423299691U 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 1 135: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 116/223 Test #33: graphmolMolOpsTest ..................... Passed 1.25 sec test 158 Start 158: testRascalCluster 158: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES 158: Test timeout computed to be: 1500 130: [07:34:58] Rep: 0 Mol:13 130: [07:34:58] Rep: 0 Mol:4 155: 155: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 155: Time elapsed 0.003918 seconds 155: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 155: 1: NOREF. Reference data NOT LISTED in test case. 155: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 155: 2: NOREF. Reference data NOT LISTED in test case. 155: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 155: 3: NOREF. Reference data NOT LISTED in test case. 155: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 155: 4: NOREF. Reference data NOT LISTED in test case. 155: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 155: 5: NOREF. Reference data NOT LISTED in test case. 146: generating reference drawings 155: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 155: 6: NOREF. Reference data NOT LISTED in test case. 155: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 155: 7: NOREF. Reference data NOT LISTED in test case. 155: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 155: 8: NOREF. Reference data NOT LISTED in test case. 130: [07:34:58] Rep: 0 Mol:7 130: [07:34:58] Rep: 0 Mol:6 155: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 155: 9: NOREF. Reference data NOT LISTED in test case. 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 155: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 155: 10: NOREF. Reference data NOT LISTED in test case. 130: [07:34:58] Rep: 0 Mol:11 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 155: 11: NOREF. Reference data NOT LISTED in test case. 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 155: 12: NOREF. Reference data NOT LISTED in test case. 132: .[07:34:58] UFFTYPER: Unrecognized hybridization for atom: 0 132: [07:34:58] UFFTYPER: Unrecognized atom type: Cu+1 (0) 155: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 155: 13: NOREF. Reference data NOT LISTED in test case. 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 148: file rxn_test1_7.png gave hash 1232578493U not the expected 528963379U 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 155: 14: NOREF. Reference data NOT LISTED in test case. 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 155: 15: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 155: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 155: 16: NOREF. Reference data NOT LISTED in test case. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 155: 17: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 155: 18: NOREF. Reference data NOT LISTED in test case. 132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 130: [07:34:58] Rep: 0 Mol:17 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 148: file rxn_test1_7.svg gave hash 798375802U not the expected 1881564163U 148: Done 148: ----------------- Test 2: some examples that caused problems in testing 130: [07:34:58] Rep: 0 Mol:15 132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 130: [07:34:58] Rep: 0 Mol:10 132: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 108: =>start test MORSE 108: =>read file 108: [07:34:58] test on : 365 molecules done 130: [07:34:58] Rep: 0 Mol:19 130: [07:34:58] Rep: 0 Mol:23 130: [07:34:58] Rep: 0 Mol:27 130: [07:34:58] Rep: 0 Mol:8 117/223 Test #108: testMORSE .............................. Passed 0.93 sec test 159 Start 159: pyMolDraw2D 159: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 159: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 159: Test timeout computed to be: 1500 125: ....... 125: ---------------------------------------------------------------------- 125: Ran 7 tests in 0.102s 125: 125: OK 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 155: ----------------------------------- 155: Time elapsed 0.004986 seconds 155: 155: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 155: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 155: 1: PASSED. matchedRefRes = 4 155: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 155: 2: PASSED. matchedRefRes = 1 155: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 155: 3: PASSED. matchedRefRes = 6 155: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 155: 4: PASSED. matchedRefRes = 13 155: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 155: 5: PASSED. matchedRefRes = 12 130: [07:34:58] Rep: 0 Mol:12 130: [07:34:58] Rep: 0 Mol:31 148: file rxn_test2_1.png gave hash 160703765U not the expected 399415052U 147: file testPNGMetadata_2.png gave hash 1862211480U not the expected 2803353117U 155: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 155: 6: PASSED. matchedRefRes = 10 155: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 155: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 155: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 155: 10: PASSED. matchedRefRes = 3 130: [07:34:58] Rep: 0 Mol:16 132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 155: 12: PASSED. matchedRefRes = 8 155: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 13: PASSED. matchedRefRes = 9 155: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 155: 14: PASSED. matchedRefRes = 11 155: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 15: PASSED. matchedRefRes = 2 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 130: [07:34:58] Rep: 0 Mol:20 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 148: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C 141: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 130: [07:34:58] Rep: 0 Mol:21 130: [07:34:58] Rep: 0 Mol:24 135: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 130: [07:34:58] Rep: 0 Mol:14 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 155: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 155: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 155: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 155: ----------------------------------- 155: 155: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 155: Time elapsed 0.005898 seconds 155: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 155: 1: PASSED. matchedRefRes = 4 155: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 155: 2: PASSED. matchedRefRes = 1 155: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 155: 3: PASSED. matchedRefRes = 6 130: [07:34:58] Rep: 0 Mol:25 130: [07:34:58] Rep: 0 Mol:28 155: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 155: 4: PASSED. matchedRefRes = 13 155: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 155: 5: PASSED. matchedRefRes = 12 155: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 155: 6: PASSED. matchedRefRes = 10 155: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 155: 7: NOREF. Reference data NOT LISTED in test case. 155: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 8: NOREF. Reference data NOT LISTED in test case. 155: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 9: NOREF. Reference data NOT LISTED in test case. 148: file rxn_test2_2_1.png gave hash 4057570363U not the expected 1215378243U 130: [07:34:58] Rep: 0 Mol:18 155: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 155: 10: PASSED. matchedRefRes = 3 155: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 11: NOREF. Reference data NOT LISTED in test case. 155: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 155: 12: PASSED. matchedRefRes = 8 155: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 13: PASSED. matchedRefRes = 9 155: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 155: 14: PASSED. matchedRefRes = 11 155: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 15: PASSED. matchedRefRes = 2 141: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 155: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 155: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 155: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 155: ----------------------------------- 155: 155: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE 155: Time elapsed 0.000893 seconds 155: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 155: 1: PASSED. matchedRefRes = 2 155: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 155: 2: PASSED. matchedRefRes = 3 148: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl 155: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 155: 3: NOREF. Reference data NOT LISTED in test case. 135: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] 155: 4: PASSED. matchedRefRes = 4 155: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 155: 5: PASSED. matchedRefRes = 5 130: [07:34:58] Rep: 0 Mol:22 155: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 155: 6: NOREF. Reference data NOT LISTED in test case. 155: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 155: 7: PASSED. matchedRefRes = 7 118/223 Test #125: pyPartialCharges ....................... Passed 0.66 sec test 160 Start 160: testCIPLabeler 160: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 160: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler 160: Test timeout computed to be: 1500 132: ... 132: ---------------------------------------------------------------------- 132: Ran 18 tests in 0.159s 132: 132: OK 130: [07:34:58] Rep: 0 Mol:29 130: [07:34:58] Rep: 0 Mol:26 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] 155: 6: CC(N1CC1)C(=O),Case1-SIMPLE,CC([*:1])[*:2],C1CN1[*:1].O=C[*:2] 155: ----------------------------------- 155: 155: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 155: Time elapsed 0.003744 seconds 155: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 155: 1: NOREF. Reference data NOT LISTED in test case. 155: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 155: 2: NOREF. Reference data NOT LISTED in test case. 155: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 155: 3: NOREF. Reference data NOT LISTED in test case. 155: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 155: 4: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 148: file rxn_test2_2_2.png gave hash 362458924U not the expected 3645141778U 155: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 155: 5: NOREF. Reference data NOT LISTED in test case. 155: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 155: 6: NOREF. Reference data NOT LISTED in test case. 155: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 155: 7: NOREF. Reference data NOT LISTED in test case. 155: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 155: 8: NOREF. Reference data NOT LISTED in test case. 155: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 155: 9: NOREF. Reference data NOT LISTED in test case. 147: file testGithub3369_1.svg gave hash 1012801087U not the expected 3091976328U 155: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 155: 10: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 148: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 148: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 148: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C 155: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 155: 11: NOREF. Reference data NOT LISTED in test case. 155: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 155: 12: NOREF. Reference data NOT LISTED in test case. 155: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 155: 13: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 155: 14: NOREF. Reference data NOT LISTED in test case. 155: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 155: 15: NOREF. Reference data NOT LISTED in test case. 155: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 155: 16: NOREF. Reference data NOT LISTED in test case. 155: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 155: 17: NOREF. Reference data NOT LISTED in test case. 155: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 155: 18: NOREF. Reference data NOT LISTED in test case. 148: file rxn_test2_2_3.png gave hash 1657316579U not the expected 551946805U 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 155: ----------------------------------- 155: 155: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 155: Time elapsed 0.003990 seconds 155: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 155: 1: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 155: 2: NOREF. Reference data NOT LISTED in test case. 130: [07:34:58] Rep: 0 Mol:30 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 155: 3: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 155: 4: NOREF. Reference data NOT LISTED in test case. 155: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 155: 5: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 155: 6: NOREF. Reference data NOT LISTED in test case. 155: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 155: 7: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 155: 8: NOREF. Reference data NOT LISTED in test case. 155: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 155: 9: NOREF. Reference data NOT LISTED in test case. 148: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC 155: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 155: 10: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 155: 11: NOREF. Reference data NOT LISTED in test case. 155: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 155: 12: NOREF. Reference data NOT LISTED in test case. 155: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 155: 13: NOREF. Reference data NOT LISTED in test case. 155: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 155: 14: PASSED. matchedRefRes = 1 155: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 155: 15: NOREF. Reference data NOT LISTED in test case. 155: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 155: 16: NOREF. Reference data NOT LISTED in test case. 155: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 155: 17: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 155: 18: NOREF. Reference data NOT LISTED in test case. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 155: --- ALL PASSED --- 155: ----------------------------------- 155: 5 TEST CASES FAILED 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 119/223 Test #155: testMMPA ............................... Passed 0.16 sec test 161 Start 161: pyCIPLabelsWrapTest 161: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 161: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 161: Test timeout computed to be: 1500 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 141: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 141: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 141: .[07:34:58] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] 141: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 141: ... 141: ---------------------------------------------------------------------- 141: Ran 9 tests in 0.092s 141: 141: OK 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 146: processing 146: launch :0 128: processing 128: launch :0 128: launch :1 128: launch :2 128: launch :3 148: file rxn_test2_2_4.png gave hash 2796626100U not the expected 4234617566U 146: launch :1 146: launch :2 146: launch :3 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 128: [07:34:58] [07:34:58] [07:34:58] Rep: 0Rep: [07:34:58] Rep: 0Rep: 0 Mol: Mol: Mol:0 128: 1 128: 0 Mol:3 128: 2 128: [07:34:58] Rep: 0 Mol:5 148: Done 148: ----------------- Test 3: test reactant highlighting 147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 128: [07:34:58] Rep: 0 Mol:9 128: [07:34:58] Rep: 0 Mol:4 147: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U 147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 120/223 Test #132: pyForceFieldHelpers .................... Passed 0.63 sec test 162 Start 162: pyCIPLabelsValidation 162: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 162: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 162: Test timeout computed to be: 1500 128: [07:34:58] Rep: 0 Mol:13 134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 5 128: [07:34:58] Rep: 0 Mol:8 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 160: Randomness seeded to: 2977283498 160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 143: . 143: ---------------------------------------------------------------------- 143: Ran 1 test in 0.082s 143: 143: OK 143: Testing Shape Helpers wrapper 128: [07:34:58] Rep: 0 Mol:17 147: file testHandDrawn-1.png gave hash 811421521U not the expected 698316547U 128: [07:34:58] Rep: 0 Mol:6 134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 5 128: [07:34:58] Rep: 0 Mol:12 97: .............[07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 128: [07:34:58] Rep: 0 Mol:10 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 128: [07:34:58] Rep: 0 Mol:7 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 128: [07:34:58] Rep: 0 Mol:16 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 128: [07:34:58] Rep: 0 Mol:11 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 148: file rxn_test3_1.png gave hash 3699939964U not the expected 4176857511U 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 128: [07:34:58] Rep: 0 Mol:15 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 128: [07:34:58] Rep: 0 Mol:19 128: [07:34:58] Rep: 0 Mol:23 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 128: [07:34:58] Rep: 0 Mol:27 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 5 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [07:34:58] dasfsadf 128: [07:34:58] Rep: 0 Mol:21 128: [07:34:58] Rep: 0 Mol:31 148: file rxn_test3_1.svg gave hash 1959543526U not the expected 2165658826U 128: [07:34:58] Rep: 0 Mol:20 148: Done 148: ----------------- Test 4: some examples from SMARTS in testing 148: draw! 145: . 145: ---------------------------------------------------------------------- 145: Ran 1 test in 0.011s 145: 145: OK 128: [07:34:58] Rep: 0 Mol:25 128: [07:34:58] Rep: 0 Mol:24 128: [07:34:58] Rep: 0 Mol:29 128: [07:34:58] Rep: 0 Mol:28 147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 121/223 Test #143: pyShapeHelpers ......................... Passed 0.48 sec test 163 Start 163: deprotectTest 163: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 163: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect 163: Test timeout computed to be: 1500 128: [07:34:58] Rep: 0 Mol:14 149: ...[07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. 149: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 122/223 Test #141: pyChemicalFeatures ..................... Passed 0.56 sec test 164 Start 164: pyDeprotect 164: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rough_test.py" 164: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 164: Test timeout computed to be: 1500 128: [07:34:58] Rep: 0 Mol:18 147: file testHandDrawn-2.svg gave hash 2224670338U not the expected 4132716144U 147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 128: [07:34:58] Rep: 0 Mol:22 123/223 Test #145: pyMolCatalog ........................... Passed 0.48 sec test 165 Start 165: testReducedGraphs 165: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 165: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs 165: Test timeout computed to be: 1500 148: file rxn_test4_1.png gave hash 1897728811U not the expected 4187207676U 128: [07:34:58] Rep: 0 Mol:26 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 147: file testHandDrawn-2.png gave hash 928126416U not the expected 1605553248U 148: file rxn_test4_1.svg gave hash 2683567127U not the expected 3239755313U 148: done 147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-3.svg gave hash 633044862U not the expected 4199337510U 147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 128: [07:34:58] Rep: 0 Mol:30 147: file testHandDrawn-3.png gave hash 2410179907U not the expected 2881952238U 147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-4.svg gave hash 2180320567U not the expected 4197407865U 147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 154: ... 154: ---------------------------------------------------------------------- 154: Ran 3 tests in 0.015s 154: 154: OK 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 165: 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 165: 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, ] 165: 97: .[07:34:58] SMILES Parse Error: syntax error while parsing: mydoghasfleas 97: [07:34:58] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 165: 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 165: 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 165: 160: =============================================================================== 160: All tests passed (5977 assertions in 13 test cases) 160: 147: file testHandDrawn-4.png gave hash 1714306199U not the expected 3431655453U 124/223 Test #160: testCIPLabeler ......................... Passed 0.25 sec test 166 Start 166: pyReducedGraphs 166: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 166: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 166: Test timeout computed to be: 1500 163: Randomness seeded to: 3508537481 163: =============================================================================== 163: All tests passed (111 assertions in 3 test cases) 163: 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 165: 125/223 Test #163: deprotectTest .......................... Passed 0.09 sec test 167 Start 167: trajectoryTest 167: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 167: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory 167: Test timeout computed to be: 1500 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 165: 165: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 165: 135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 126/223 Test #165: testReducedGraphs ...................... Passed 0.08 sec test 168 Start 168: substructLibraryTest 168: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 168: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 168: Test timeout computed to be: 1500 134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 6 149: ..........[07:34:58] 149: 149: **** 149: Pre-condition Violation 149: molecule must not be None 149: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp 149: Failed Expression: m 149: **** 149: 148: file rxn_test4_2.png gave hash 3724924058U not the expected 3490081297U 134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 6 127/223 Test #154: pyMolHash .............................. Passed 0.44 sec test 169 Start 169: substructLibraryCatchTest 169: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 169: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 169: Test timeout computed to be: 1500 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 168: [07:34:59] ------------------------------------- 168: [07:34:59] Test1 134: [07:34:59] UFFTYPER: Unrecognized charge state for atom: 6 148: file rxn_test4_2.svg gave hash 4278906476U not the expected 4127054729U 148: Done 128/223 Test #148: moldraw2DRxnTest1 ...................... Passed 0.58 sec test 170 Start 170: pySubstructLibrary 170: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 170: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 170: Test timeout computed to be: 1500 106: =>start test morse custom 106: [07:34:59] test on : 365 molecules done 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 128: [07:34:59] Rep: 20 Mol:3 128: [07:34:59] Rep: 20 Mol:7 128: [07:34:59] Rep: 20 Mol:11 128: [07:34:59] Rep: 20 Mol:15 128: [07:34:59] Rep: 20 Mol:19 128: [07:34:59] Rep: 20 Mol:23 128: [07:34:59] Rep: 20 Mol:27 128: [07:34:59] Rep: 20 Mol:31 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 119: [07:34:59] done 119: [07:34:59] ------------------------------------- 119: [07:34:59] Test GitHub Issue #6958 97: ....... 97: ---------------------------------------------------------------------- 97: Ran 21 tests in 1.125s 97: 97: OK 97: (Five aromatic carbons And (Not any of Five aromatic carbons)) 97: (Five aromatic carbons Or (Not any of Five aromatic carbons)) 97: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) 97: ******************************************** 97: Testing: PAINS_A 2 97: ******************************************** 97: Testing: PAINS_B 4 97: ******************************************** 97: Testing: PAINS_C 8 97: ******************************************** 97: Testing: PAINS 14 97: (Not FilterMatcher) 97: Bar 97: Count 1 97: ******************************************** 97: {'Cl,Br,I'} 97: 1 97: 2 97: running 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 129/223 Test #119: testFingerprintGenerators .............. Passed 1.13 sec test 171 Start 171: testRGroupDecomp 171: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 171: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 171: Test timeout computed to be: 1500 128: [07:34:59] Rep: 20 Mol:1 128: [07:34:59] Rep: 20 Mol:5 128: [07:34:59] Rep: 20 Mol:9 128: [07:34:59] Rep: 20 Mol:13 128: [07:34:59] Rep: 20 Mol:17 128: [07:34:59] Rep: 20 Mol:21 128: [07:34:59] Rep: 20 Mol:25 128: [07:34:59] Rep: 20 Mol:29 130: [07:34:59] Rep: 100 Mol:0 130: [07:34:59] Rep: 100 Mol:4 130: [07:34:59] Rep: 100 Mol:8 130: [07:34:59] Rep: 100 Mol:12 130: [07:34:59] Rep: 100 Mol:16 130: [07:34:59] Rep: 100 Mol:20 130: [07:34:59] Rep: 100 Mol:24 130: [07:34:59] Rep: 100 Mol:28 161: ... 161: ---------------------------------------------------------------------- 161: Ran 3 tests in 0.024s 161: 161: OK 128: [07:34:59] Rep: 20 Mol:0 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 128: [07:34:59] Rep: 20 Mol:4 128: [07:34:59] Rep: 20 Mol:8 128: [07:34:59] Rep: 20 Mol:12 128: [07:34:59] Rep: 20 Mol:16 128: [07:34:59] Rep: 20 Mol:20 128: [07:34:59] Rep: 20 Mol:24 128: [07:34:59] Rep: 20 Mol:28 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 149: ..................... 149: ---------------------------------------------------------------------- 149: Ran 34 tests in 0.397s 149: 149: OK 149: json lasso 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 130/223 Test #97: pyFilterCatalog ........................ Passed 1.60 sec test 172 Start 172: testRGroupDecompInternals 172: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 172: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 172: Test timeout computed to be: 1500 128: [07:34:59] Rep: 40 Mol:3 128: [07:34:59] Rep: 40 Mol:7 128: [07:34:59] Rep: 40 Mol:11 131/223 Test #161: pyCIPLabelsWrapTest .................... Passed 0.51 sec test 173 Start 173: rgroupCatchTests 173: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 173: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 173: Test timeout computed to be: 1500 128: [07:34:59] Rep: 40 Mol:15 128: [07:34:59] Rep: 40 Mol:19 128: [07:34:59] Rep: 40 Mol:23 128: [07:34:59] Rep: 40 Mol:27 128: [07:34:59] Rep: 40 Mol:31 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 128: [07:34:59] Rep: 20 Mol:2 168: [07:34:59] done 128: [07:34:59] Rep: 20 Mol:6 128: [07:34:59] Rep: 20 Mol:10 128: [07:34:59] Rep: 20 Mol:14 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 128: [07:34:59] Rep: 20 Mol:18 128: [07:34:59] Rep: 20 Mol:22 128: [07:34:59] Rep: 20 Mol:26 168: [07:34:59] ------------------------------------- 168: [07:34:59] Test2 128: [07:34:59] Rep: 20 Mol:30 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 132/223 Test #149: pyMolDraw2D ............................ Passed 0.91 sec test 174 Start 174: pyRGroupDecomposition 174: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 174: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 174: Test timeout computed to be: 1500 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 130: [07:34:59] Rep: 100 Mol:3 130: [07:34:59] Rep: 100 Mol:7 130: [07:34:59] Rep: 100 Mol:11 130: [07:34:59] Rep: 100 Mol:15 130: [07:34:59] Rep: 100 Mol:19 133/223 Test #172: testRGroupDecompInternals .............. Passed 0.10 sec test 175 Start 175: molInterchangeTest1 175: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 175: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 175: Test timeout computed to be: 1500 130: [07:34:59] Rep: 100 Mol:23 130: [07:34:59] Rep: 100 Mol:27 130: [07:34:59] Rep: 100 Mol:31 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 135: .[07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 166: ..... 166: ---------------------------------------------------------------------- 166: Ran 5 tests in 0.017s 166: 166: OK 175: [07:34:59] test1: basics 175: [07:34:59] done 175: [07:34:59] test2: basic writing 175: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[0,0]}]}]} 175: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 175: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 175: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} 175: [07:34:59] done 175: [07:34:59] test3: writing conformers 175: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1987,-0.0452],[-0.3332,0.4555],[0.1659,1.322],[0.5332,-0.0438],[-2.0652,0.4541],[-0.8339,1.3212]]},{"dim":3,"coords":[[0.9553,-0.3743,-0.4679],[-0.3616,-0.131,-0.0794],[-0.5097,1.6255,0.1705],[-0.5778,-0.7919,1.1042],[1.5276,0.1063,0.1627],[-1.0339,-0.4345,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2023.09.3","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} 175: [07:34:59] done 175: [07:34:59] test4: writing properties 175: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[0,0]}]}]} 175: [07:34:59] done 175: [07:34:59] test5: writing partial charges 175: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2023.09.3","values":[0.5,-0.5]}]}]} 175: [07:34:59] testing parse options 175: [07:34:59] done 175: [07:34:59] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 175: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} 175: [07:34:59] done 175: [07:34:59] testing 'either' stereochemistry 175: [07:34:59] done 134/223 Test #175: molInterchangeTest1 .................... Passed 0.07 sec test 176 Start 176: molInterchangeCatchTest 176: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 176: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 176: Test timeout computed to be: 1500 135/223 Test #166: pyReducedGraphs ........................ Passed 0.49 sec test 177 Start 177: pyMolInterchange 177: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 177: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 177: Test timeout computed to be: 1500 176: Randomness seeded to: 2932294546 128: [07:34:59] Rep: 60 Mol:3 128: [07:34:59] Rep: 60 Mol:7 128: [07:34:59] Rep: 60 Mol:11 128: [07:34:59] Rep: 60 Mol:15 128: [07:34:59] Rep: 60 Mol:19 128: [07:34:59] Rep: 60 Mol:23 128: [07:34:59] Rep: 60 Mol:27 128: [07:34:59] Rep: 60 Mol:31 176: [07:34:59] unrecognized bond type 12 set to zero while writing 176: [07:34:59] unrecognized bond type 0 set to zero while writing 176: =============================================================================== 176: All tests passed (117 assertions in 5 test cases) 176: 136/223 Test #176: molInterchangeCatchTest ................ Passed 0.05 sec test 178 Start 178: testSLNParse 178: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 178: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 178: Test timeout computed to be: 1500 178: [07:34:59] SLN Parse Error: syntax error while parsing: CH4[I=13] 178: [07:34:59] Failed parsing SLN 'CH4[I=13]' 164: ..... 164: ---------------------------------------------------------------------- 164: Ran 5 tests in 0.049s 164: 164: OK 164: Testing tert-butyldimethylsilyl 164: Testing methoxytrityl 164: Testing tetrahydropyranyl 164: Testing methoxymethyl_ether 164: Testing beta-Methoxyethoxymethyl_ether 164: Testing benzyl 164: Testing trimethylsilyl 164: Testing benzoyl 164: Testing pivaloyl 164: Testing triisopropylsilyl 164: Testing acetyl 164: Testing para-methoxybenzyl_ether 164: Testing triphenylmethyl 164: Testing phthaloyl 164: Testing trimethylsilylethoxymethyl 164: Testing para-methoxyphenyl 164: Testing tosyl 164: Testing tert-butyloxycarbonyl 164: Testing trifluoroacetyl 164: Testing benzoyl 164: Testing 9-fluorenylmethyloxycarbonyl 164: Testing benzylamine 164: Testing acetamide 164: Testing carbobenzyloxy 164: Testing Acetal/Ketal 164: Testing tert-butyldimethylsilyl 164: Testing methoxytrityl 164: Testing tetrahydropyranyl 164: Testing methoxymethyl_ether 164: Testing beta-Methoxyethoxymethyl_ether 164: Testing benzyl 164: Testing trimethylsilyl 164: Testing benzoyl 164: Testing pivaloyl 164: Testing triisopropylsilyl 164: Testing acetyl 164: Testing para-methoxybenzyl_ether 164: Testing triphenylmethyl 164: Testing phthaloyl 164: Testing trimethylsilylethoxymethyl 164: Testing para-methoxyphenyl 164: Testing tosyl 164: Testing tert-butyloxycarbonyl 164: Testing trifluoroacetyl 164: Testing benzoyl 164: Testing 9-fluorenylmethyloxycarbonyl 164: Testing benzylamine 164: Testing acetamide 164: Testing carbobenzyloxy 164: Testing Acetal/Ketal 178: [07:34:59] SLN Parser error: Atom ID 1 appears *after* its ring closure. 178: [07:34:59] SLN Parser error: Ring closure 1 does not have a corresponding opener. 178: [07:34:59] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) 178: [07:34:59] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' 178: [07:34:59] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) 178: [07:34:59] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' 178: [07:34:59] SLN Parse Error: syntax error while parsing: CH4 fff 178: [07:34:59] Failed parsing SLN 'CH4 fff' 178: [07:34:59] SLN Parse Error: syntax error while parsing: C[charge=+1] foo 178: [07:34:59] Failed parsing SLN 'C[charge=+1] foo' 128: [07:34:59] Rep: 40 Mol:1 178: [07:34:59] Query property 'is' ignored on non-query atom 128: [07:34:59] Rep: 40 Mol:5 178: [07:34:59] Query property 'is' ignored on non-query atom 128: [07:34:59] Rep: 40 Mol:9 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 173: Randomness seeded to: 3346413248 173: =============================================================================== 173: All tests passed (203 assertions in 13 test cases) 173: 137/223 Test #178: testSLNParse ........................... Passed 0.05 sec test 179 Start 179: pySLNParse 179: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" 179: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap 179: Test timeout computed to be: 1500 138/223 Test #173: rgroupCatchTests ....................... Passed 0.28 sec test 180 Start 180: pyGraphMolWrap 180: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rough_test.py" 180: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 180: Test timeout computed to be: 1500 128: [07:34:59] Rep: 40 Mol:13 128: [07:34:59] Rep: 40 Mol:17 128: [07:34:59] Rep: 40 Mol:21 128: [07:34:59] Rep: 40 Mol:25 128: [07:34:59] Rep: 40 Mol:29 139/223 Test #167: trajectoryTest ......................... Passed 0.62 sec test 181 Start 181: pyTestConformerWrap 181: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testConformer.py" 181: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 181: Test timeout computed to be: 1500 140/223 Test #164: pyDeprotect ............................ Passed 0.71 sec test 182 Start 182: pyTestTrajectory 182: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testTrajectory.py" 182: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 182: Test timeout computed to be: 1500 128: [07:34:59] Rep: 40 Mol:0 106: =>start test AUTOCORR3D custom 106: [07:34:59] test on : 365 molecules done 169: Randomness seeded to: 1579871511 169: =============================================================================== 169: All tests passed (171 assertions in 5 test cases) 169: 128: [07:34:59] Rep: 40 Mol:4 128: [07:34:59] Rep: 40 Mol:8 128: [07:34:59] Rep: 40 Mol:12 128: [07:34:59] Rep: 40 Mol:16 141/223 Test #169: substructLibraryCatchTest .............. Passed 0.65 sec test 183 Start 183: pyTestSGroups 183: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testSGroups.py" 183: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 183: Test timeout computed to be: 1500 128: [07:34:59] Rep: 40 Mol:2 128: [07:34:59] Rep: 40 Mol:6 128: [07:34:59] Rep: 40 Mol:10 128: [07:34:59] Rep: 40 Mol:20 128: [07:34:59] Rep: 40 Mol:14 128: [07:34:59] Rep: 40 Mol:24 128: [07:34:59] Rep: 40 Mol:18 128: [07:34:59] Rep: 40 Mol:28 128: [07:34:59] Rep: 40 Mol:22 128: [07:34:59] Rep: 40 Mol:26 128: [07:34:59] Rep: 40 Mol:30 128: [07:34:59] Rep: 80 Mol:3 128: [07:34:59] Rep: 80 Mol:7 128: [07:34:59] Rep: 80 Mol:11 128: [07:34:59] Rep: 80 Mol:15 128: [07:34:59] Rep: 80 Mol:19 128: [07:34:59] Rep: 80 Mol:23 128: [07:34:59] Rep: 80 Mol:27 128: [07:34:59] Rep: 80 Mol:31 168: [07:34:59] done 168: [07:34:59] ------------------------------------- 168: [07:34:59] Test3 (stereo options) 171: [07:34:59] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters 135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() 171: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors 130: [07:34:59] Rep: 100 Mol:1 130: [07:34:59] Rep: 100 Mol:5 130: [07:34:59] Rep: 100 Mol:9 130: [07:34:59] Rep: 100 Mol:13 130: [07:34:59] Rep: 100 Mol:17 130: [07:34:59] Rep: 100 Mol:21 130: [07:34:59] Rep: 100 Mol:25 130: [07:34:59] Rep: 100 Mol:29 106: =>start test 2 WHIM custom 106: [07:34:59] test on : 365 molecules done 147: file testHandDrawn-5a.svg gave hash 3172919116U not the expected 3628607349U 147: [07:34:59] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 168: [07:34:59] Done (stereo options) 168: [07:34:59] ------------------------------------- 168: [07:34:59] Test4 (trusted smiles) 147: file testHandDrawn-5b.svg gave hash 3290430369U not the expected 2522138089U 147: [07:34:59] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [07:34:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 128: [07:34:59] Rep: 60 Mol:1 128: [07:34:59] Rep: 60 Mol:5 128: [07:34:59] Rep: 60 Mol:9 128: [07:34:59] Rep: 60 Mol:13 128: [07:34:59] Rep: 60 Mol:17 128: [07:34:59] Rep: 60 Mol:21 128: [07:34:59] Rep: 60 Mol:25 128: [07:34:59] Rep: 60 Mol:29 26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 168: [07:34:59] Done (trusted smiles) 168: [07:34:59] ------------------------------------- 168: [07:34:59] Testing C++ docs 168: [07:34:59] Done (C++ doc tests) 168: [07:34:59] ------------------------------------- 168: [07:34:59] Testing C++ ring query: PatternHolder 168: [07:34:59] Done (C++ ring query tests) 168: [07:34:59] ------------------------------------- 168: [07:34:59] Testing C++ ring query: TautomerPatternHolder 168: [07:34:59] Done (C++ ring query tests) 168: [07:34:59] ------------------------------------- 168: [07:34:59] Add Patterns 87: . 87: ---------------------------------------------------------------------- 87: Ran 11 tests in 1.997s 87: 87: OK 87: True 87: == CartesianProductStrategy CartesianProductStrategy 87: 197 out of 300 87: 0 6 out of 10 87: 1 3 out of 5 87: 2 4 out of 6 87: 198 out of 300 87: 0 10 out of 10 87: 1 5 out of 5 87: 2 6 out of 6 87: Skipped 10000000 in 0.0670316219329834 seconds 87: Skipped 10000000 in 0.9053530693054199 seconds 87: Skipped 10000000 in 0.6273438930511475 seconds 147: file testHandDrawn-5.png gave hash 2408781090U not the expected 3439548169U 179: .. 179: ---------------------------------------------------------------------- 179: Ran 2 tests in 0.023s 179: 179: OK 147: file testBrackets-5a.svg gave hash 4023768529U not the expected 3061667963U 130: [07:35:00] Rep: 100 Mol:2 130: [07:35:00] Rep: 100 Mol:6 130: [07:35:00] Rep: 100 Mol:10 130: [07:35:00] Rep: 100 Mol:14 130: [07:35:00] Rep: 100 Mol:18 130: [07:35:00] Rep: 100 Mol:22 130: [07:35:00] Rep: 100 Mol:26 130: [07:35:00] Rep: 100 Mol:30 147: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 147: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 147: file testPositionVariation-1b.svg gave hash 823876785U not the expected 174339626U 128: [07:35:00] Rep: 60 Mol:0 128: [07:35:00] Rep: 60 Mol:4 128: [07:35:00] Rep: 60 Mol:8 177: .. 177: ---------------------------------------------------------------------- 177: Ran 2 tests in 0.034s 177: 177: OK 26: All 191 tests passed 128: [07:35:00] Rep: 60 Mol:12 128: [07:35:00] Rep: 60 Mol:16 128: [07:35:00] Rep: 60 Mol:20 128: [07:35:00] Rep: 60 Mol:24 128: [07:35:00] Rep: 60 Mol:28 142/223 Test #179: pySLNParse ............................. Passed 0.55 sec test 184 Start 184: pyTestThreads 184: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testThreads.py" 184: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 184: Test timeout computed to be: 1500 128: [07:35:00] Rep: 60 Mol:2 128: [07:35:00] Rep: 60 Mol:6 128: [07:35:00] Rep: 60 Mol:10 182: [07:35:00] 182: 182: **** 182: Pre-condition Violation 182: from must be < size() 182: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: from < static_cast(size()) 182: **** 182: 182: .[07:35:00] 182: 182: **** 182: Pre-condition Violation 182: from must be < size() 182: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: from < static_cast(size()) 182: **** 182: 128: [07:35:00] Rep: 60 Mol:14 128: [07:35:00] Rep: 60 Mol:18 143/223 Test #87: pyChemReactionEnumerations ............. Passed 2.49 sec test 185 Start 185: pyTestMultithreadedMolSupplier 185: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 185: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 185: Test timeout computed to be: 1500 128: [07:35:00] Rep: 60 Mol:22 128: [07:35:00] Rep: 60 Mol:26 128: [07:35:00] Rep: 60 Mol:30 147: [07:35:00] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U 183: ............. 183: ---------------------------------------------------------------------- 183: Ran 13 tests in 0.054s 183: 183: OK 183: Testing SubstanceGroups wrapper 147: file testGithub4238_1.png gave hash 1562907664U not the expected 3410617836U 135: [07:35:00] Molecule does not have explicit Hs. Consider calling AddHs() 147: file testGithub4323_1.png gave hash 3600756148U not the expected 3723958844U 106: =>start test 1 WHIM custom 106: [07:35:00] test on : 365 molecules done 144/223 Test #177: pyMolInterchange ....................... Passed 0.77 sec test 186 Start 186: pyTestPropertyLists 186: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testPropertyLists.py" 186: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 186: Test timeout computed to be: 1500 145/223 Test #183: pyTestSGroups .......................... Passed 0.57 sec test 187 Start 187: pyCDXMLTest 187: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/test_cdxml.py" 187: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 187: Test timeout computed to be: 1500 26: 26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... 128: [07:35:00] Rep: 80 Mol:1 128: [07:35:00] Rep: 80 Mol:5 128: [07:35:00] Rep: 80 Mol:9 128: [07:35:00] Rep: 80 Mol:13 128: [07:35:00] Rep: 80 Mol:17 128: [07:35:00] Rep: 80 Mol:21 128: [07:35:00] Rep: 80 Mol:25 128: [07:35:00] Rep: 80 Mol:29 181: ...... 181: ---------------------------------------------------------------------- 181: Ran 6 tests in 0.028s 181: 181: OK 180: ..............[07:35:00] SMARTS Parse Error: syntax error while parsing: fiib 180: [07:35:00] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' 147: file testGithub4323_3.png gave hash 1951856443U not the expected 2185913679U 182: .[07:35:00] 182: 182: **** 182: Range Error 182: snapshotNum 182: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: 0 < 0 182: **** 182: 182: .[07:35:00] 182: 182: **** 182: Pre-condition Violation 182: The trajectory must have dimension == 3 182: Violation occurred on line 113 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: traj.dimension() == 3 182: **** 182: 182: ..[07:35:00] 182: 182: **** 147: [07:35:00] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 182: Pre-condition Violation 182: The trajectory must have dimension == 3 182: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: traj.dimension() == 3 182: **** 182: 182: .[07:35:00] 182: 182: **** 182: Pre-condition Violation 182: d_pos must not be NULL 182: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: d_pos 182: **** 182: 182: [07:35:00] 182: 182: **** 182: Pre-condition Violation 182: d_trajectory must not be NULL 182: Violation occurred on line 24 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: d_trajectory 182: **** 182: 182: .[07:35:00] 182: 182: **** 182: Range Error 182: snapshotNum 182: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: 5 < 5 182: **** 182: 128: [07:35:00] Rep: 80 Mol:0 182: [07:35:00] 182: 182: **** 182: Range Error 182: pointNum 182: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: 10 < 10 128: [07:35:00] Rep: 80 Mol:4 182: **** 182: 182: .[07:35:00] 182: 182: **** 182: Range Error 182: snapshotNum 182: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: 5 < 5 128: [07:35:00] Rep: 80 Mol:8 182: **** 182: 182: [07:35:00] 182: 182: **** 128: [07:35:00] Rep: 80 Mol:12 182: Pre-condition Violation 182: d_dimension must be == 2 182: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: d_trajectory->dimension() == 2 128: [07:35:00] Rep: 80 Mol:16 182: **** 182: 182: [07:35:00] 182: 182: **** 182: Pre-condition Violation 182: d_dimension must be == 2 182: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: d_trajectory->dimension() == 2 128: [07:35:00] Rep: 80 Mol:20 180: ....[07:35:00] ERROR: Problems encountered parsing data fields 180: [07:35:00] ERROR: moving to the beginning of the next molecule 180: [07:35:00] ERROR: Problems encountered parsing data fields 180: [07:35:00] ERROR: moving to the beginning of the next molecule 180: [07:35:00] Spurious data before the first property will be ignored 180: [07:35:00] Property will be truncated after the first blank line 180: [07:35:00] Property will be truncated after the first blank line 180: [07:35:00] Property will be truncated after the first blank line 146/223 Test #181: pyTestConformerWrap .................... Passed 0.82 sec test 188 Start 188: molStandardizeTest 188: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 188: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 188: Test timeout computed to be: 1500 180: [07:35:00] ERROR: Problems encountered parsing data fields 180: [07:35:00] ERROR: moving to the beginning of the next molecule 180: [07:35:00] ERROR: Problems encountered parsing data fields 180: [07:35:00] ERROR: moving to the beginning of the next molecule 180: [07:35:00] Spurious data before the first property will be ignored 180: [07:35:00] Property will be truncated after the first blank line 180: [07:35:00] Property will be truncated after the first blank line 180: [07:35:00] Property will be truncated after the first blank line 180: [07:35:00] ERROR: Problems encountered parsing data fields 180: [07:35:00] ERROR: moving to the beginning of the next molecule 180: [07:35:00] Property will be truncated after the first blank line 180: [07:35:00] ERROR: Problems encountered parsing data fields 180: [07:35:00] ERROR: moving to the beginning of the next molecule 180: [07:35:00] Property will be truncated after the first blank line 182: **** 182: 182: . 182: ---------------------------------------------------------------------- 182: Ran 9 tests in 0.320s 182: 182: OK 182: Testing Trajectory wrapper 128: [07:35:00] Rep: 80 Mol:24 128: [07:35:00] Rep: 80 Mol:28 180: .[07:35:00] SMILES Parse Error: syntax error while parsing: fail 180: [07:35:00] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 180: [07:35:00] ERROR: Smiles parse error on line 2 180: [07:35:00] ERROR: Cannot create molecule from : 'fail' 180: >>> This may result in an infinite loop. It should finish almost instantly 180: <<< OK, it finished. 147/223 Test #182: pyTestTrajectory ....................... Passed 0.87 sec test 189 Start 189: molNormalizeTest 189: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 189: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 189: Test timeout computed to be: 1500 180: ............[07:35:00] Explicit valence for atom # 1 C, 5, is greater than permitted 128: [07:35:00] Rep: 80 Mol:2 128: [07:35:00] Rep: 80 Mol:6 128: [07:35:00] Rep: 80 Mol:10 128: [07:35:00] Rep: 80 Mol:14 128: [07:35:00] Rep: 80 Mol:18 128: [07:35:00] Rep: 80 Mol:22 128: [07:35:00] Rep: 80 Mol:26 128: [07:35:00] Rep: 80 Mol:30 180: ............[07:35:00] non-ring atom 0 marked aromatic 180: [07:35:00] non-ring atom 0 marked aromatic 180: [07:35:00] 180: 180: **** 180: Range Error 180: idx 180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp 180: Failed Expression: 12 < 6 180: **** 180: 180: [07:35:00] non-ring atom 0 marked aromatic 180: [07:35:00] non-ring atom 0 marked aromatic 189: [07:35:00] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 180: [07:35:00] 180: 180: **** 180: Range Error 180: idx 180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp 180: Failed Expression: 12 < 6 180: **** 180: 180: ...............[07:35:00] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 111: =>start test GETAWAY 111: [07:35:00] test on : 365 molecules done 180: [07:35:00] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 148/223 Test #111: testGETAWAY ............................ Passed 2.75 sec test 190 Start 190: molValidateTest 190: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 190: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 190: Test timeout computed to be: 1500 138: 2030076355 135: [07:35:00] Molecule does not have explicit Hs. Consider calling AddHs() 180: ..............[07:35:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 180: [07:35:00] Explicit valence for atom # 1 C, 5, is greater than permitted 189: [07:35:00] Initializing Normalizer 189: [07:35:00] Running Normalizer 189: [07:35:00] Rule applied: BrokenazidetoN=N+=N- 189: [07:35:00] Initializing Normalizer 189: [07:35:00] Running Normalizer 189: [07:35:00] Initializing Normalizer 189: [07:35:00] Running Normalizer 149/223 Test #189: molNormalizeTest ....................... Passed 0.18 sec test 191 Start 191: molChargeTest 191: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 191: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 191: Test timeout computed to be: 1500 187: . 187: ---------------------------------------------------------------------- 187: Ran 1 test in 0.026s 187: 187: OK 150/223 Test #190: molValidateTest ........................ Passed 0.09 sec test 192 Start 192: molTautomerTest 192: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 192: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 192: Test timeout computed to be: 1500 151/223 Test #38: hanoiTest .............................. Passed 3.27 sec test 193 Start 193: molStandardizeSmallTest 193: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 193: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 193: Test timeout computed to be: 1500 150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 150: Time elapsed 0.000 seconds 150: 150: test32() 150: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds 150: Time elapsed 0.068 seconds 150: 150: test190() 150: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds 150: Time elapsed 0.010 seconds 150: 150: test3() 150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds 150: Time elapsed 0.015 seconds 150: 150: testSimpleFast() 150: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds 150: Time elapsed 0.113 seconds 150: 150: testSimple() 150: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 150: Time elapsed 0.108 seconds 150: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 150: Time elapsed 0.154 seconds 150: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds 150: Time elapsed 0.113 seconds 150: 150: testSegFault() 150: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 150: Time elapsed 0.011 seconds 150: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 150: Time elapsed 0.031 seconds 150: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds 150: Time elapsed 0.026 seconds 150: 150: testThreshold() 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: Time elapsed 0.000 seconds 150: 150: testRing1() 150: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds 150: Time elapsed 0.569 seconds 150: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds 150: Time elapsed 0.489 seconds 150: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds 150: Time elapsed 0.450 seconds 150: 150: testAtomCompareIsotopes() 150: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds 150: Time elapsed 0.000 seconds 150: 150: testAtomCompareAnyAtom() 150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 150: Time elapsed 0.000 seconds 150: 150: testAtomCompareAnyAtom() 150: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds 150: Time elapsed 0.000 seconds 150: 150: testAtomCompareAnyAtom() 150: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds 150: Time elapsed 0.000 seconds 150: 150: testAtomCompareAnyAtom() 150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds 150: Time elapsed 0.000 seconds 150: 150: testJnk1LigandsDistance() 150: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds 150: Time elapsed 0.014 seconds 150: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds 152/223 Test #193: molStandardizeSmallTest ................ Passed 0.07 sec test 194 Start 194: molFragmentTest 194: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 194: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 194: Test timeout computed to be: 1500 153/223 Test #187: pyCDXMLTest ............................ Passed 0.51 sec test 195 Start 195: molStandardizeCatchTest 195: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 195: Test timeout computed to be: 1500 154/223 Test #191: molChargeTest .......................... Passed 0.12 sec test 196 Start 196: pyMolStandardize 196: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 196: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 196: Test timeout computed to be: 1500 128: [07:35:00] done 128: [07:35:00] ------------------------------------- 128: [07:35:00] Test MMFF multithreading2 186: [07:35:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 186: [07:35:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 186: [07:35:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 186: .[07:35:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 186: [07:35:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 186: [07:35:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 186: ...[07:35:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 186: [07:35:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 186: [07:35:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 186: . 186: ---------------------------------------------------------------------- 186: Ran 5 tests in 0.019s 186: 186: OK 130: [07:35:00] done 130: [07:35:00] ------------------------------------- 130: [07:35:00] Test UFF multithreading2 185: .s. 185: ---------------------------------------------------------------------- 185: Ran 3 tests in 0.222s 185: 185: OK (skipped=1) 185: Testing Smiles and SD MultithreadedMolSupplier 194: [07:35:00] SMARTS Parse Error: syntax error while parsing: [Cl 194: [07:35:00] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' 155/223 Test #194: molFragmentTest ........................ Passed 0.14 sec test 197 Start 197: testScaffoldNetwork 197: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 197: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork 197: Test timeout computed to be: 1500 156/223 Test #186: pyTestPropertyLists .................... Passed 0.67 sec test 198 Start 198: pyScaffoldNetwork 198: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 198: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 198: Test timeout computed to be: 1500 150: Time elapsed 0.001 seconds 150: 150: test18() 150: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 150: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds 150: Time elapsed 0.016 seconds 150: 150: test504() 150: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 150: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds 150: Time elapsed 0.214 seconds 150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 150: Time elapsed 0.001 seconds 150: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds 150: Time elapsed 0.093 seconds 150: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds 150: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0047 seconds. bond[0]=6 150: STATISTICS: 150: Total Growing Steps = 1, MCS found on 1 step, for 0.0047 seconds 150: Initial Seeds = 1, Mismatched 0 150: Inspected Seeds = 2 150: Rejected by BestSize = 0 150: IndividualBondExcluded = 0 150: MatchCheck Seeds = 2 150: MatchCalls = 2 150: MatchFound = 1 150: fastMatchCalls = 1 150: fastMatchFound = 0 150: slowMatchCalls = 2 150: slowMatchFound = 1 150: DupCacheFound = 0 0 matched, 0 mismatched 150: HashCache size = 1 keys 150: HashCache size = 1 entries 150: FindHashInCache = 2 150: HashFoundInCache= 0 150: ExactMatchCalls = 0 150: ExactMatchFound = 0 150: Time elapsed 0.005 seconds 150: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 150: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 150: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 150: res sub = 1 size=3 150: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 150: res sub = 1 size=3 150: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 150: test target = CC[C@H](F)Cl query = CCC useChirality = 0 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = CC[C@H](F)Cl query = CCC useChirality = 1 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = CCC(F)Cl query = CC useChirality = 0 150: res sub = 1 size=2 150: MCS: [#6]-[#6] 2 atoms, 1 bonds 150: test target = CCC(F)Cl query = CC useChirality = 1 150: res sub = 1 size=2 150: MCS: [#6]-[#6] 2 atoms, 1 bonds 150: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 157/223 Test #185: pyTestMultithreadedMolSupplier ......... Passed 0.97 sec test 199 Start 199: pyScaffoldNetworkPickling 199: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 199: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 199: Test timeout computed to be: 1500 150: res sub = 1 size=4 150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 150: res sub = 0 size=0 150: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 150: res sub = 0 size=0 150: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 150: res sub = 0 size=0 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = OC(F)CCl query = OC(F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = OC(F)CCl query = OC(F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 150: res sub = 0 size=0 150: MCS: [#9] 1 atoms, 0 bonds 150: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 150: res sub = 0 size=0 150: MCS: [#9] 1 atoms, 0 bonds 150: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 150: res sub = 1 size=3 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 150: res sub = 1 size=3 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 150: res sub = 1 size=3 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 150: res sub = 1 size=3 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: 150: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> 150: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: done 195: Randomness seeded to: 2462257919 195: * - * - * - * m1 135: [07:35:01] Molecule does not have explicit Hs. Consider calling AddHs() 195: * - * - * - * m2 195: * - * - * - * m1 195: * - * - * - * m2 159: ........ 159: ---------------------------------------------------------------------- 159: Ran 8 tests in 2.050s 159: 159: OK 195: [07:35:01] Can't kekulize mol. Unkekulized atoms: 3 7 195: [07:35:01] Can't kekulize mol. Unkekulized atoms: 3 8 195: [07:35:01] Can't kekulize mol. Unkekulized atoms: 2 3 4 128: [07:35:01] done 128: [07:35:01] ------------------------------------- 128: [07:35:01] Test MMFF multithreading3 156: ......... 156: ---------------------------------------------------------------------- 156: Ran 9 tests in 2.294s 156: 156: OK 158/223 Test #159: pyMolDraw2D ............................ Passed 2.57 sec test 200 Start 200: testMolEnumerator 200: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 200: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator 200: Test timeout computed to be: 1500 130: [07:35:01] done 130: [07:35:01] ------------------------------------- 130: [07:35:01] Test UFF multithreading3 147: file testFlexiCanvas.2a.png gave hash 3809318030U not the expected 3217758043U 147: file testFlexiCanvas.2b.png gave hash 1941040420U not the expected 4070063910U 159/223 Test #156: pyMMPA ................................. Passed 2.66 sec test 201 Start 201: pyMolEnumerator 201: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 201: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 201: Test timeout computed to be: 1500 134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 147: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U 200: Randomness seeded to: 1216860012 200: [07:35:01] can only enumerate SRUs with CONNECT=HT or CONNECT=HH 200: =============================================================================== 200: All tests passed (321 assertions in 16 test cases) 200: 160/223 Test #200: testMolEnumerator ...................... Passed 0.24 sec test 202 Start 202: testAbbreviations 202: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 202: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations 202: Test timeout computed to be: 1500 147: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U 147: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U 147: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U 198: ....... 198: ---------------------------------------------------------------------- 198: Ran 7 tests in 0.047s 198: 198: OK 147: file testGithub4764.sz1.png gave hash 1936053216U not the expected 98827714U 134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 64: [07:35:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 64: [07:35:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 202: Randomness seeded to: 3211858611 202: [07:35:01] SMARTS Parse Error: syntax error while parsing: *fail 202: [07:35:01] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' 147: file testGithub4764.sz2.png gave hash 518440428U not the expected 89252465U 161/223 Test #198: pyScaffoldNetwork ...................... Passed 0.66 sec test 203 Start 203: pyAbbreviations 203: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 203: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 203: Test timeout computed to be: 1500 202: [07:35:01] no suitable SubstanceGroups found 202: =============================================================================== 202: All tests passed (195 assertions in 12 test cases) 202: 133: building molecules 162/223 Test #202: testAbbreviations ...................... Passed 0.08 sec test 204 Start 204: generalizedSubstructCatch 204: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 204: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 204: Test timeout computed to be: 1500 133: generating reference data 128: [07:35:01] done 128: [07:35:01] ------------------------------------- 128: [07:35:01] Testing github 162: Incorrect SMILES after MMFF parameterization . 128: [07:35:01] done 128: [07:35:01] ------------------------------------- 128: [07:35:01] Testing github 224: crash during MMFF parameterization . 128: [07:35:01] done 128: [07:35:01] ------------------------------------- 128: [07:35:01] Testing github6728: crash due to missing stretch-bend params. 163/223 Test #128: testMMFFForceFieldHelpers .............. Passed 3.54 sec test 205 Start 205: pyGeneralizedSubstruct 205: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 205: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 205: Test timeout computed to be: 1500 199: . 199: ---------------------------------------------------------------------- 199: Ran 1 test in 0.015s 199: 199: OK 138: 959503528 138: =============================================================================== 138: All tests passed (73 assertions in 3 test cases) 138: 134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 130: [07:35:01] done 130: [07:35:01] ------------------------------------- 130: [07:35:01] Testing GitHubIssue62. 164/223 Test #138: molAlignCatchTest ...................... Passed 3.35 sec test 206 Start 206: testQuery 206: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Query/testQuery 206: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Query 206: Test timeout computed to be: 1500 130: [07:35:01] beta-lactam 39.6387 130: [07:35:01] cyclopropanone 174.698 206: Query 206: Query2 206: Equality 206: Greater 206: GreaterEqual 206: Less 206: LessEqual 206: Open Range 206: Closed Range 206: Float 206: With Tolerance 206: Set 206: And 206: Or 206: XOr 206: pointer and copy foo 206: Set2 147: file testGithub4764.sz3.png gave hash 1437648833U not the expected 148503574U 165/223 Test #206: testQuery .............................. Passed 0.01 sec test 207 Start 207: testMatCalc 207: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 207: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc 207: Test timeout computed to be: 1500 130: [07:35:01] aziridine 337.986 130: [07:35:01] aziridinone 115.248 130: [07:35:01] isobutene 2.48217 130: [07:35:01] acetone 1.91788 207: 1.68022e+08 207: 1.73149e+08 207: 1.05549e+08 207: 7.20603e+07 207: 1.41535e+08 207: 1.08592e+08 207: 1.11334e+08 207: 2.05553e+08 207: 1.54962e+08 207: 8.08231e+07 207: 5.61421e+07 207: 1.28874e+08 207: 1.59011e+08 207: 8.69902e+07 207: 1.31367e+08 207: 2.27389e+08 207: 1.60289e+08 207: 7.79813e+07 207: 1.61001e+08 207: 2.07599e+08 207: 2.24432e+08 207: 1.39725e+08 207: 2.42614e+08 207: 1.77578e+08 207: 1.05908e+08 207: 9.06742e+07 207: 1.8087e+08 207: 1.98182e+08 207: 2.03052e+08 207: 1.7673e+08 207: 9.32798e+07 207: 1.37969e+08 207: 1.83778e+08 207: 2.1228e+08 207: 5.06157e+07 207: 1.566e+08 207: 2.37142e+08 207: 1.49345e+08 207: 7.05819e+07 207: 1.71633e+08 207: 1.96817e+08 207: 2.18246e+08 207: 9.49496e+07 207: 2.25618e+08 207: 1.30219e+08 166/223 Test #207: testMatCalc ............................ Passed 0.01 sec test 208 Start 208: pyMatCalc 208: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 208: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 208: Test timeout computed to be: 1500 130: [07:35:01] cyclopentanone 10.1648 130: [07:35:01] cyclopropene 99.4921 130: [07:35:01] cyclobutene 41.0156 130: [07:35:01] cyclopropane 267.236 147: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U 130: [07:35:01] gamma-lactam 15.7471 167/223 Test #199: pyScaffoldNetworkPickling .............. Passed 0.60 sec test 209 Start 209: testSimDivPickers 209: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers 209: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers 209: Test timeout computed to be: 1500 209: [07:35:01] ------------------------------------- 209: [07:35:01] Testing github issue 1421: MaxMinPicker picking non-existent element. 209: [07:35:01] Done 209: [07:35:01] ------------------------------------- 209: [07:35:01] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. 209: [07:35:01] Done 168/223 Test #209: testSimDivPickers ...................... Passed 0.02 sec test 210 Start 210: pickersTestsCatch 210: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 210: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers 210: Test timeout computed to be: 1500 64: ---------------------------------- 64: ---------------------------------- 64: [07:35:01] 64: 64: **** 64: Pre-condition Violation 64: rlabel out of range for MDL files 64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp 64: Failed Expression: rlabel >= 0 && rlabel < 100 64: **** 64: 64: [07:35:01] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 130: [07:35:01] trans-2,3-diphenylcyclopropan-1-one 203.398 147: file github5383_1.svg gave hash 2850811663U not the expected 3666750661U 147: file github5383_2.svg gave hash 1346330069U not the expected 0U 130: [07:35:01] cis-2,3-diphenylcyclopropan-1-one 206.852 147: file github5383_1.png gave hash 3128184037U not the expected 992803933U 147: file acs1996_1.png gave hash 1346742279U not the expected 2957839025U 130: [07:35:01] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 147: file acs1996_2.png gave hash 806461087U not the expected 2664798808U 130: [07:35:01] cyclopropylidencyclobutane 218.879 147: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U 201: ... 201: ---------------------------------------------------------------------- 201: Ran 3 tests in 0.015s 201: 201: OK 130: [07:35:01] diphenylmethylidencyclobutane 79.6139 130: [07:35:01] done 130: [07:35:01] ------------------------------------- 130: [07:35:01] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. 130: [07:35:01] done 130: [07:35:01] ------------------------------------- 174: .................. 174: ---------------------------------------------------------------------- 174: Ran 18 tests in 1.955s 174: 174: OK 130: [07:35:01] Test square planar complexes 130: [07:35:01] done 130: [07:35:01] ------------------------------------- 130: [07:35:01] Test octahedral complexes 130: [07:35:01] done 169/223 Test #130: testUFFForceFieldHelpers ............... Passed 3.72 sec test 211 Start 211: pySimDivPickers 211: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/testPickers.py" 211: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap 211: Test timeout computed to be: 1500 147: [07:35:01] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. 134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 210: Randomness seeded to: 2522949967 210: =============================================================================== 210: All tests passed (21267 assertions in 1 test case) 210: 170/223 Test #210: pickersTestsCatch ...................... Passed 0.14 sec test 212 Start 212: pyRanker 212: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/testRanker.py" 212: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap 212: Test timeout computed to be: 1500 204: Randomness seeded to: 1845426689 204: =============================================================================== 204: All tests passed (180 assertions in 10 test cases) 204: 171/223 Test #204: generalizedSubstructCatch .............. Passed 0.28 sec test 213 Start 213: testChemicalFeatures 213: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 213: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures 213: Test timeout computed to be: 1500 134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 147: file bond_highlights_8.svg gave hash 682598716U not the expected 2956924065U 213: ----------------------------------------- 213: Test1 213: Done 172/223 Test #201: pyMolEnumerator ........................ Passed 0.58 sec 173/223 Test #213: testChemicalFeatures ................... Passed 0.01 sec test 214 Start 214: pyFeatures 214: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/testFeatures.py" 214: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap 214: Test timeout computed to be: 1500 test 215 Start 215: pythonTestDbCLI 215: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/Projects" 215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Projects 215: Test timeout computed to be: 1500 174/223 Test #174: pyRGroupDecomposition .................. Passed 2.52 sec test 216 Start 216: pythonTestDirRoot 216: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit" 216: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit 216: Test timeout computed to be: 1500 134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 175/223 Test #40: resMolSupplierTest ..................... Passed 4.50 sec test 217 Start 217: pythonTestDirML 217: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/ML/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/ML" 217: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit 217: Test timeout computed to be: 1500 203: ....... 203: ---------------------------------------------------------------------- 203: Ran 7 tests in 0.022s 203: 203: OK 147: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U 176/223 Test #203: pyAbbreviations ........................ Passed 0.43 sec test 218 Start 218: pythonTestDirDataStructs 218: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs" 218: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit 218: Test timeout computed to be: 1500 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test Issue252: Bad definitions for Crippen atom types. 147: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test calculation of ChiVs. 147: file github6504_2.svg gave hash 106020287U not the expected 2871662880U 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test calculation of ChiNs. 147: file github6569_1.svg gave hash 1698514747U not the expected 116573839U 147: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test calculation of HallKierAlpha. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test calculation of Kappa1. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test calculation of Kappa2. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test calculation of Kappa3. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test Crippen atom type calculations. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test ring descriptors 147: file lasso_highlights_1.svg gave hash 2411984833U not the expected 689837467U 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test other count descriptors. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test MQN 147: file lasso_highlights_2.svg gave hash 1109702647U not the expected 348394942U 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test GitHub Issue 56. 100: [07:35:02] WARNING: not removing hydrogen atom without neighbors 100: [07:35:02] WARNING: not removing hydrogen atom without neighbors 100: [07:35:02] WARNING: not removing hydrogen atom without neighbors 100: [07:35:02] WARNING: not removing hydrogen atom without neighbors 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test Github92: Bad Crippen atom type for pyrrole H. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test Github362: order dependence in Kier-Hall descriptors. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test calculation of spiro and bridgehead counts. 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test Github694: ExactMolWt ignoring the mass of the electron 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Testing Properties and KitchenSink 64: [07:35:02] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 64: [07:35:02] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 147: file lasso_highlights_3.svg gave hash 2940545227U not the expected 2174136207U 100: [07:35:02] ---Caught keyerror (bad property name)--- 100: [07:35:02] ---Caught stereo value error--- 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test USR Descriptor 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test Github #1973: support P and S terms for TPSA calculation 100: [07:35:02] done 100: [07:35:02] ------------------------------------- 100: [07:35:02] Test Github #2948: Empty molecule has non-zero LabuteASA 100: [07:35:02] done 147: file lasso_highlights_4.svg gave hash 3276894790U not the expected 1265047504U 177/223 Test #100: testDescriptors ........................ Passed 4.44 sec test 219 Start 219: pythonTestDirDbase 219: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase" 219: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit 219: Test timeout computed to be: 1500 147: file lasso_highlights_5.svg gave hash 2028645321U not the expected 35778943U 147: file lasso_highlights_6.svg gave hash 1732575234U not the expected 1359376880U 147: file lasso_highlights_7.svg gave hash 1593492996U not the expected 773081917U 196: .....[07:35:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached 64: [07:35:02] Empty atom list: 'M ALS 1 0 F' on line 8. 64: de_DE.UTF-8 64: [07:35:02] ------------------------------------- 64: [07:35:02] Test multithreading Locale Switching 192: [07:35:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached 214: .. 214: ---------------------------------------------------------------------- 214: Ran 2 tests in 0.001s 214: 214: OK 214: Testing ChemicalFeatures Wrapper code: 135: [07:35:02] Molecule does not have explicit Hs. Consider calling AddHs() 147: file bad_lasso_1.svg gave hash 1431427975U not the expected 1183031575U 147: =============================================================================== 147: All tests passed (6525 assertions in 94 test cases) 147: 178/223 Test #147: moldraw2DTestCatch ..................... Passed 3.79 sec test 220 Start 220: pythonTestDirSimDivFilters 220: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters" 220: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit 220: Test timeout computed to be: 1500 211: [07:35:02] the useCache argument is deprecated and ignored 64: [07:35:02] Test multithreading (Done) 64: [07:35:02] ------------------------------------- 212: ..[07:35:02] 212: 212: **** 212: Invariant Violation 212: Can't rank more bits than the ensemble size 212: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp 212: Failed Expression: num <= dp_maskBits->getNumOnBits() 212: **** 212: 212: ... 212: ---------------------------------------------------------------------- 212: Ran 5 tests in 0.022s 212: 212: OK 179/223 Test #214: pyFeatures ............................. Passed 0.37 sec test 221 Start 221: pythonTestDirVLib 221: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/VLib" 221: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit 221: Test timeout computed to be: 1500 64: *************************************** 64: *************************************** 64: [07:35:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [07:35:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 196: [07:35:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 180/223 Test #212: pyRanker ............................... Passed 0.43 sec test 222 Start 222: pythonTestSping 222: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/sping" 222: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit 222: Test timeout computed to be: 1500 64: [07:35:02] bond with order 0 found on line 7. This is not part of the MDL specification. 64: [07:35:02] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 64: [07:35:02] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 64: [07:35:02] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML import BuildComposite 64: generating smiles 64: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 64: converting back 64: check isomorphism 205: ....... 205: ---------------------------------------------------------------------- 205: Ran 7 tests in 0.189s 205: 205: OK 135: [07:35:02] Molecule does not have explicit Hs. Consider calling AddHs() 181/223 Test #188: molStandardizeTest ..................... Passed 1.95 sec test 223 Start 223: pythonTestDirChem 223: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Chem" "--buildType" "None" 223: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem 223: Test timeout computed to be: 1500 182/223 Test #205: pyGeneralizedSubstruct ................. Passed 0.77 sec 219: .. 219: ---------------------------------------------------------------------- 219: Ran 2 tests in 0.050s 219: 219: OK 211: ...[07:35:02] the useCache argument is deprecated and ignored 211: [07:35:02] the useCache argument is deprecated and ignored 211: .[07:35:02] the useCache argument is deprecated and ignored 218: ....... 218: ---------------------------------------------------------------------- 218: Ran 7 tests in 0.023s 218: 218: OK 208: ..... 208: ---------------------------------------------------------------------- 208: Ran 5 tests in 0.334s 208: 208: OK 216: ......................... 216: ---------------------------------------------------------------------- 216: Ran 25 tests in 0.396s 216: 216: OK 183/223 Test #208: pyMatCalc .............................. Passed 0.84 sec 196: .[07:35:02] Tautomer enumeration stopped at 63 tautomers: canceled 196: Enumeration was canceled due to timeout (50 ms) 221: ............. 221: ---------------------------------------------------------------------- 221: Ran 13 tests in 0.035s 221: 221: OK 184/223 Test #216: pythonTestDirRoot ...................... Passed 0.67 sec 135: [07:35:02] Molecule does not have explicit Hs. Consider calling AddHs() 150: [07:35:02] The provided InitialSeed is not an MCS and will be ignored 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: refCompos = pickle.load(pklF) 158: Randomness seeded to: 3297325481 158: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi 219: ........... 219: ---------------------------------------------------------------------- 219: Ran 11 tests in 0.123s 219: 219: OK 192: [07:35:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached 135: [07:35:02] Molecule does not have explicit Hs. Consider calling AddHs() 218: .................................. 218: ---------------------------------------------------------------------- 218: Ran 34 tests in 0.010s 218: 218: OK 197: Randomness seeded to: 1810421622 197: =============================================================================== 197: All tests passed (269 assertions in 19 test cases) 197: 185/223 Test #197: testScaffoldNetwork .................... Passed 1.95 sec 186/223 Test #220: pythonTestDirSimDivFilters ............. Passed 0.62 sec 137: *********************************************************** 137: Testing O3AAlign 137: --------------------------------- 137: testMMFFO3A 137: 137: --------------------------------- 137: testMMFFO3A with pre-computed dmat and MolHistogram 137: 137: --------------------------------- 137: testMMFFO3A with constraints 137: 137: --------------------------------- 137: testMMFFO3A with variable weight constraints followed by local-only optimization 137: 137: --------------------------------- 137: testCrippenO3A 137: 137: --------------------------------- 137: testCrippenO3A with pre-computed dmat and MolHistogram 137: 137: --------------------------------- 137: testCrippenO3A with constraints 137: 137: --------------------------------- 137: testCrippenO3A with variable weight constraints followed by local-only optimization 137: 137: --------------------------------- 137: testMMFFO3A multithreading 137: 137: generating reference data 192: [07:35:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 219: . 219: ---------------------------------------------------------------------- 219: Ran 1 test in 0.001s 219: 219: OK 106: =>start test GETAWAY custom 106: [07:35:03] test on : 365 molecules done 187/223 Test #106: testRDFcustom .......................... Passed 5.31 sec 135: [07:35:03] Molecule does not have explicit Hs. Consider calling AddHs() 219: FF......F...... 219: ====================================================================== 219: FAIL: test1Txt (__main__.TestCase.test1Txt) 219: test reading from a text file 219: ---------------------------------------------------------------------- 219: Traceback (most recent call last): 219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt 219: self._confirm(tblName, dbName=self.tempDbName) 219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm 219: assert len(res) == len(colHeads), 'bad number of columns' 219: ^^^^^^^^^^^^^^^^^^^^^^^^^ 219: AssertionError: bad number of columns 219: 219: ====================================================================== 219: FAIL: test3Txt (__main__.TestCase.test3Txt) 219: test reading from a text file including null markers 219: ---------------------------------------------------------------------- 219: Traceback (most recent call last): 219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt 219: self._confirm(tblName, dbName=self.tempDbName) 219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm 219: assert len(res) == len(colHeads), 'bad number of columns' 219: ^^^^^^^^^^^^^^^^^^^^^^^^^ 219: AssertionError: bad number of columns 219: 219: ====================================================================== 219: FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) 219: ---------------------------------------------------------------------- 219: Traceback (most recent call last): 219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase 219: self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) 219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm 219: assert len(res) == len(colHeads), 'bad number of columns' 219: ^^^^^^^^^^^^^^^^^^^^^^^^^ 219: AssertionError: bad number of columns 219: 219: ---------------------------------------------------------------------- 219: Ran 15 tests in 0.074s 219: 219: FAILED (failures=3) 223: ....... 223: ---------------------------------------------------------------------- 223: Ran 7 tests in 0.167s 223: 223: OK 192: [07:35:03] Tautomer enumeration stopped at 25 tautomers: canceled 192: Enumeration was canceled due to timeout (50 ms) 135: [07:35:03] Molecule does not have explicit Hs. Consider calling AddHs() 217: ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: refCompos = pickle.load(pklFile) 219: ...... 219: ---------------------------------------------------------------------- 219: Ran 6 tests in 0.006s 219: 219: OK 221: ........... 221: ---------------------------------------------------------------------- 221: Ran 11 tests in 0.111s 221: 221: OK 219: !!! TEST FAILURE: python UnitTestDbUtils.py {} 188/223 Test #219: pythonTestDirDbase .....................***Failed 1.25 sec .. ---------------------------------------------------------------------- Ran 2 tests in 0.050s OK ........... ---------------------------------------------------------------------- Ran 11 tests in 0.123s OK . ---------------------------------------------------------------------- Ran 1 test in 0.001s OK FF......F...... ====================================================================== FAIL: test1Txt (__main__.TestCase.test1Txt) test reading from a text file ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt self._confirm(tblName, dbName=self.tempDbName) File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm assert len(res) == len(colHeads), 'bad number of columns' ^^^^^^^^^^^^^^^^^^^^^^^^^ AssertionError: bad number of columns ====================================================================== FAIL: test3Txt (__main__.TestCase.test3Txt) test reading from a text file including null markers ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt self._confirm(tblName, dbName=self.tempDbName) File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm assert len(res) == len(colHeads), 'bad number of columns' ^^^^^^^^^^^^^^^^^^^^^^^^^ AssertionError: bad number of columns ====================================================================== FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm assert len(res) == len(colHeads), 'bad number of columns' ^^^^^^^^^^^^^^^^^^^^^^^^^ AssertionError: bad number of columns ---------------------------------------------------------------------- Ran 15 tests in 0.074s FAILED (failures=3) ...... ---------------------------------------------------------------------- Ran 6 tests in 0.006s OK !!! TEST FAILURE: python UnitTestDbUtils.py {} 215: [07:35:03] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:03] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:03] INFO: Processing 10 molecules 215: 217: . 217: ---------------------------------------------------------------------- 217: Ran 6 tests in 0.715s 217: 217: OK 222: .. 222: ---------------------------------------------------------------------- 222: Ran 2 tests in 0.567s 222: 222: OK 211: ....... 211: ---------------------------------------------------------------------- 211: Ran 11 tests in 1.261s 211: 211: OK 12: .................. 12: ---------------------------------------------------------------------- 12: Ran 18 tests in 5.912s 12: 12: OK 215: [07:35:03] INFO: Generating fingerprints and descriptors: 215: 189/223 Test #12: pyBV ................................... Passed 6.16 sec 190/223 Test #221: pythonTestDirVLib ...................... Passed 1.30 sec 218: ..... 218: ---------------------------------------------------------------------- 218: Ran 5 tests in 0.044s 218: 218: OK 26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 191/223 Test #211: pySimDivPickers ........................ Passed 1.72 sec 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML import ScreenComposite 26: All 191 tests passed 215: [07:35:03] INFO: Finished. 215: 171: iterative 223: ...... 223: ---------------------------------------------------------------------- 223: Ran 6 tests in 0.047s 223: 223: OK 192/223 Test #222: pythonTestSping ........................ Passed 1.50 sec 26: 26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: compos = pickle.load(pklF) 217: ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: compos = pickle.load(pklF) 64: [07:35:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [07:35:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [07:35:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [07:35:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [07:35:03] deprecated group abbreviation ignored on line 24 64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 64: [07:35:03] 64: 64: **** 64: Post-condition Violation 64: Element 'Mv' not found 64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 64: Failed Expression: anum > -1 64: **** 64: 168: [07:35:03] ------------------------------------- 168: [07:35:03] testing PatternHolder 217: .......... 217: ---------------------------------------------------------------------- 217: Ran 12 tests in 0.164s 217: 217: OK 218: ....... 218: ---------------------------------------------------------------------- 218: Ran 7 tests in 0.006s 218: 218: OK 196: Enumeration has completed 196: [07:35:04] Tautomer enumeration stopped at 48 tautomers: canceled 193/223 Test #218: pythonTestDirDataStructs ............... Passed 2.22 sec 168: [07:35:04] ------------------------------------- 168: [07:35:04] testing TautomerPatternHolder 133: validating reference data 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML import AnalyzeComposite 223: ....[07:35:04] 223: 223: **** 223: Pre-condition Violation 223: valence not defined for atoms not associated with molecules 223: Violation occurred on line 411 in file ./Code/GraphMol/Atom.cpp 223: Failed Expression: dp_mol 223: **** 223: 223: . 223: ---------------------------------------------------------------------- 223: Ran 5 tests in 0.031s 223: 223: OK 192: 375 192: Enumeration has completed 192: [07:35:04] Tautomer enumeration stopped at 48 tautomers: canceled 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: c1 = pickle.load(pklF) 168: [07:35:04] ------------------------------------- 168: [07:35:04] testSegFaultInHolder 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: dsafsdf 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] [07:35:04] SMILES Parse Error: syntax error[07:35:04] [07:35:04] [07:35:04] 168: dsafsdf[07:35:04] SMILESSMILES Parse Error: SMILES Parse Error: syntax errorsyntax error' while parsing: SMILES Parse Error: while parsing: 168: dsafsdf 168: while parsing: dsafsdf 168: syntax error[07:35:04] dsafsdfSMILES 168: while parsing: SMILES Parse Error: dsafsdf 168: [07:35:04] [07:35:04] [07:35:04] SMILES Parse Error: syntax error while parsing: syntax error[07:35:04] Parse Error: SMILES Parse Error: [07:35:04] [07:35:04] SMILES Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES for input: ' Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf'dsafsdf[07:35:04] syntax error while parsing: dsafsdf 168: 'SMILES Parse Error: 168: SMILESsyntax error while parsing: for input: 'dsafsdfdsafsdf' 168: while parsing: for input: ' Parse Error: syntax error while parsing: dsafsdf 168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] SMILES Parse Error: dsafsdf'dsafsdf 168: 168: dsafsdfFailed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: ' 168: for input: 'dsafsdf 168: [07:35:04] SMILES[07:35:04] [07:35:04] 168: SMILESSMILES Parse Error: dsafsdfsyntax error' while parsing: dsafsdf 168: [07:35:04] 168: SMILES Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] [07:35:04] syntax errorSMILES Parse Error: [07:35:04] syntax errorSMILESSMILESSMILESdsafsdf for input: 'dsafsdf' 168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: '' while parsing: Parse Error: dsafsdf 168: Failed parsing SMILES 'dsafsdf'dsafsdf' 168: 168: for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] [07:35:04] SMILESSMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] [07:35:04] SMILES Parse Error: dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: 'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: dsafsdfFailed parsing SMILES 'dsafsdf'' for input: ' 168: ' 168: dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] [07:35:04] SMILES Parse Error: syntax error[07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: [07:35:04] SMILES Parse Error: syntax error while parsing: syntax error while parsing: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: dsafsdf 168: [07:35:04] SMILES[07:35:04] Parse Error: Failed parsing SMILES 'dsafsdf'SMILES for input: 'dsafsdf' 168: dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf 168: ' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 217: . 217: ---------------------------------------------------------------------- 217: Ran 1 test in 0.044s 217: 217: OK 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf[07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILESSMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: [07:35:04] [07:35:04] [07:35:04] [07:35:04] [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: [07:35:04] [07:35:04] [07:35:04] SMILES Parse Error: [07:35:04] [07:35:04] [07:35:04] [07:35:04] SMILES Parse Error: syntax error[07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[07:35:04] Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: [07:35:04] syntax error[07:35:04] while parsing: dsafsdf 168: SMILES Parse Error: SMILES Parse Error: [07:35:04] syntax error while parsing: while parsing: dsafsdfdsafsdfSMILES Parse Error: ' for input: 'SMILES Parse Error: syntax errorsyntax errorsyntax error 168: while parsing: SMILES Parse Error: SMILES Parse Error: [07:35:04] SMILESsyntax error Parse Error: SMILES Parse Error: 168: syntax error while parsing: [07:35:04] dsafsdfSMILES Parse Error: syntax error while parsing: 168: dsafsdf 168: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: 'dsafsdf'[07:35:04] while parsing: SMILES while parsing: dsafsdf 168: while parsing: dsafsdfSMILES Parse Error: 168: syntax errordsafsdf[07:35:04] dsafsdf Parse Error: SMILES Parse Error: 168: 168: dsafsdf[07:35:04] ' 168: SMILES Parse Error: 168: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: syntax errorSMILESFailed parsing SMILES 'dsafsdf'[07:35:04] syntax errorSMILES Parse Error: while parsing: dsafsdfsyntax errordsafsdf while parsing: dsafsdfsyntax error 168: [07:35:04] for input: '[07:35:04] [07:35:04] 168: SMILESSMILES Parse Error: syntax errordsafsdf' Parse Error: ' while parsing: SMILES[07:35:04] while parsing: while parsing: [07:35:04] dsafsdf 168: SMILES Parse Error: syntax error while parsing: dsafsdf[07:35:04] 168: syntax errorsyntax errorSMILES while parsing: dsafsdf 168: dsafsdf Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' 168: for input: 'dsafsdfSMILESdsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' Parse Error: 168: 168: 168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error while parsing: ' 168: dsafsdf 168: 168: for input: ' while parsing: dsafsdfFailed parsing SMILES 'dsafsdf'' 168: for input: 'dsafsdfdsafsdf 168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: 168: ' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] syntax errorSMILES[07:35:04] [07:35:04] [07:35:04] SMILES[07:35:04] SMILES Parse Error: [07:35:04] while parsing: SMILESdsafsdf Parse Error: Parse Error: SMILESFailed parsing SMILES 'dsafsdf'[07:35:04] 168: SMILES for input: '[07:35:04] Failed parsing SMILES 'dsafsdf' Parse Error: for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf' for input: 'dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf' 168: dsafsdfSMILES' 168: for input: 'dsafsdf' 168: ' 168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES[07:35:04] SMILES Parse Error: syntax error Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' while parsing: dsafsdf 168: dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: SMILES Parse Error: syntax error while parsing: 168: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 135: .[07:35:04] Molecule does not have explicit Hs. Consider calling AddHs() 137: processing 137: launch :0 137: launch :1 137: launch :2 137: launch :3 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [07:35:04] ------------------------------------- 168: [07:35:04] Results do not depend on numThreads 67: [07:35:04] Finished: testSmiCorrectness() 67: [07:35:04] ----------------------------------------- 67: 67: [07:35:04] 67: ----------------------------------------- 67: [07:35:04] Spurious data before the first property will be ignored 67: [07:35:04] [07:35:04] Property will be truncated after the first blank line 67: Property will be truncated after the first blank line 67: [07:35:04] Property will be truncated after the first blank line 171: bulk 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Test GitHub Issue 258: Bad pattern fingerprint for query molecule 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Test unfolded version of RDKFP 117: [07:35:04] ------------------------------------- 117: [07:35:04] Test bitinfo of RDKFP 117: 562: [ 2 ], 117: 709: [ 0 1 ], 117: 1118: [ 0 1 2 ], 117: 1183: [ 1 2 ], 117: 1233: [ 0 1 2 ], 117: 1308: [ 0 ], [ 1 ], 117: 1339: [ 2 ], 117: 1728: [ 1 2 ], 117: 1772: [ 0 ], [ 1 ], 117: 1813: [ 0 1 ], 117: ------------ 117: [07:35:04] ------------------------------------- 117: [07:35:04] Single atoms setting radius 1 bits in Morgan fingerprints 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Github #879: Pattern fingerprint should set bits for single-atom fragments. 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Github #2115: BitInfo not complete for RDKFingerprint 117: [07:35:04] done 117: [07:35:04] ------------------------------------- 117: [07:35:04] Github #3723: Fingerprint crash for mols with Zero order bonds 117: [07:35:04] done 194/223 Test #117: testFingerprints ....................... Passed 6.81 sec 196: ....................[07:35:04] Explicit valence for atom # 1 O, 3, is greater than permitted 196: . 196: ---------------------------------------------------------------------- 196: Ran 27 tests in 3.310s 196: 196: OK 196: done 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.024s 223: 223: OK 151: ........................................[07:35:05] The provided InitialSeed is not an MCS and will be ignored 151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored 151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored 195/223 Test #196: pyMolStandardize ....................... Passed 4.26 sec 151: .[07:35:05] The provided InitialSeed is not an MCS and will be ignored 151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored 151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored 151: .[07:35:05] The provided InitialSeed is not an MCS and will be ignored 151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored 151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored 192: CN=c1cc[nH]cn1 192: CN=c1ccnc[nH]1 192: CNc1ccncn1 192: res: CNc1ccncn1 192: CN=c1cccc[nH]1 192: CNc1ccccn1 192: res: CNc1ccccn1 151: .[07:35:05] The provided InitialSeed is not an MCS and will be ignored 151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored 215: [07:35:05] INFO: Reading molecules and constructing molecular database. 215: 217: ... 151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored 217: ---------------------------------------------------------------------- 217: Ran 3 tests in 0.002s 217: 217: OK 215: [07:35:05] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:05] INFO: Processing 163 molecules 215: 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: [07:35:05] Finished: testSDCorrectness() 67: [07:35:05] ----------------------------------------- 67: 196/223 Test #67: testMultithreadedMolSupplier ........... Passed 7.64 sec 151: ................. 151: ---------------------------------------------------------------------- 151: Ran 60 tests in 6.286s 151: 151: OK 197/223 Test #151: pyFMCS ................................. Passed 6.72 sec 198/223 Test #192: molTautomerTest ........................ Passed 4.67 sec 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.012s 223: 223: OK 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 180: ...........................[07:35:05] unable to set wavy bonds for double bonds: 3 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 180: .........[07:35:05] 180: 180: **** 180: Range Error 180: idx 180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp 180: Failed Expression: 6 < 5 180: **** 180: 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:05] INFO: done 100 215: 195: =============================================================================== 195: All tests passed (18691 assertions in 41 test cases) 195: 199/223 Test #195: molStandardizeCatchTest ................ Passed 4.92 sec 217: ........ 217: ---------------------------------------------------------------------- 217: Ran 8 tests in 0.001s 217: 217: OK 223: ...................... 223: ---------------------------------------------------------------------- 223: Ran 22 tests in 0.039s 223: 223: OK 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.Composite import Composite 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node 64: [07:35:06] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 64: [07:35:06] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 64: ---------------------------------- 64: ---------------------------------- 64: [07:35:06] 64: 64: **** 64: Pre-condition Violation 64: rlabel out of range for MDL files 64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp 64: Failed Expression: rlabel >= 0 && rlabel < 100 64: **** 64: 64: [07:35:06] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 223: .....s.................ss 223: ---------------------------------------------------------------------- 223: Ran 25 tests in 0.115s 223: 223: OK (skipped=3) 146: Done 146: ----------------- Test Github #781: Rendering single-atom molecules 146: Done 146: ----------------- Test 3 146: file test3_1.png gave hash 312151313U not the expected 3984824963U 146: file test3_2.png gave hash 2567824136U not the expected 238321316U 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.328s 217: 217: OK 146: file test3_3.png gave hash 527793981U not the expected 414888185U 200/223 Test #184: pyTestThreads .......................... Passed 6.44 sec 146: file test3_4.png gave hash 1225446657U not the expected 2265825690U 133: processing 133: launch :0 133: launch :1 133: launch :2 133: launch :3 64: [07:35:06] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 64: [07:35:06] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 146: file test3_5.png gave hash 4191147962U not the expected 1911551403U 146: file test3_6.png gave hash 628781660U not the expected 577293879U 146: file test3_7.png gave hash 765801686U not the expected 248355372U 146: Done 146: ----------------- Test Github774: upside-down drawings 146: file test774_1.png gave hash 1357227033U not the expected 927423591U 64: [07:35:06] Empty atom list: 'M ALS 1 0 F' on line 8. 201/223 Test #64: fileParsersTest1 ....................... Passed 9.13 sec 146: file test774_2.png gave hash 2459987343U not the expected 1171827286U 146: Done 146: ----------------- Test 9 (molecule legends) 146: file test9_1.svg gave hash 923579170U not the expected 1484349178U 146: Done 146: ----------------- Test Github852: Lines used to wedge bonds are too thick 215: [07:35:06] INFO: Generating fingerprints and descriptors: 215: 146: file test852_1.png gave hash 945814889U not the expected 736085072U 146: file test852_2.png gave hash 1614071321U not the expected 1438089260U 146: ---------------- 146: ---------------- 146: ---------------- 146: ---------------- 146: Done 146: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right 146: file test860_1.png gave hash 193088816U not the expected 2065140854U 146: file test860_2.png gave hash 3878334438U not the expected 3098360765U 146: file test860_3.png gave hash 1363134754U not the expected 3439618110U 146: Done 146: ----------------- Test Github #910: ugly coordinates generated for peptide chains 146: Done 146: ----------------- Test Github #932: mistake in SVG for wedged bonds 146: Done 146: ----------------- Test Github #953: default color should not be cyan 146: Done 146: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly 146: Done 146: ----------------- Test Deuterium, Tritium 146: Done 146: ----------------- Test crossed bonds 146: Done 146: ----------------- Testing drawing a second molecule 146: file test10_5.svg gave hash 1068653509U not the expected 1334786394U 146: file test10_6.svg gave hash 2996130233U not the expected 961103536U 146: Done 146: ----------------- Testing drawing a grid of molecules 146: Done 146: ----------------- Testing drawMolecules 146: file test12_1.svg gave hash 2982175789U not the expected 881731720U 180: ...................[07:35:06] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:06] Explicit valence for atom # 6 F, 2, is greater than permitted 180: [07:35:06] Can't kekulize mol. Unkekulized atoms: 3 4 5 146: Done 146: ----------------- Test JSON Configuration 146: Done 146: ----------------- Testing github 1090: escape html characters in SVG output 146: Done 146: ----------------- Testing github 1035: overflow bug in SVG color generation 146: Done 146: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes 146: Done 146: ----------------- Testing github 1322: add custom atom labels 146: Done 146: ----------------- Testing use of a black & white palette 146: Done 146: ----------------- Testing use of continuous highlighting with drawMolecules 146: Done 146: ----------------- Test 17 - Testing maximum font size 146: Done 146: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list 146: Done 146: ----------------- Testing use of fixed scales for drawing. 180: ...............[07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 146: Done 146: ----------------- Testing rotation of 2D drawing. 146: Done 146: ----------------- Testing inclusion of molecule metadata 146: Done 146: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default 146: Done 146: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions 146: file testGithub2151_1.svg gave hash 3620378781U not the expected 4119581143U 146: file testGithub2151_2.svg gave hash 3896781930U not the expected 425960913U 146: Done 146: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn 146: Done 146: ----------------- Testing testGithub2931: multi-coloured molecule highlights. 146: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U 146: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U 146: Done 146: ----------------- Testing annotation of 2D Drawing. 146: file test20_1.png gave hash 3128373795U not the expected 1672353490U 146: file test20_2.png gave hash 4290694897U not the expected 1073213605U 223: ..s 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.143s 223: 223: OK (skipped=1) 146: file test20_3.png gave hash 2552889633U not the expected 471234756U 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 0.002s 217: 217: OK 146: file test20_4.png gave hash 1903980179U not the expected 2803490234U 146: Done 146: ----------------- Test 21 - different font 146: Done 146: ----------------- Test 22 - draw explicit methyls. 146: Done 146: ----------------- Testing drawing of legends. 146: Done 146: ----------------- Test Github 3305 - change and scale line widths. 146: file testGithub3305_1.png gave hash 3050910344U not the expected 1801411420U 146: file testGithub3305_2.png gave hash 3318976613U not the expected 2904846519U 146: file testGithub3305_3.png gave hash 2285309697U not the expected 2915229647U 146: file testGithub3305_4.png gave hash 4191147962U not the expected 1911551403U 146: file testGithub3305_5.png gave hash 2872233459U not the expected 614319597U 146: file testGithub3305_5.svg gave hash 911738919U not the expected 3435115096U 146: file testGithub3305_6.png gave hash 829607741U not the expected 3926947401U 146: file testGithub3305_7.png gave hash 1385372926U not the expected 1720405002U 146: Done 146: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. 146: Done 146: ----------------- Test Github 4156 - bad scale for radicals in grid 146: Done 146: ----------------- Test JSON atomColourPalette 146: Done 146: ----------------- Test draw aromatic OR queries 146: Done 146: ----------------- Test AND queries 146: Done 202/223 Test #146: moldraw2DTest1 ......................... Passed 8.68 sec 217: ......... 217: ---------------------------------------------------------------------- 217: Ran 9 tests in 0.004s 217: 217: OK 171: bulk, no symmetry 217: ............ 217: ---------------------------------------------------------------------- 217: Ran 12 tests in 0.002s 217: 217: OK 171: [07:35:07] Relabelling existing label 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 0.017s 217: 217: OK 162: VS001: PASSED 162: VS002: PASSED 162: VS003: PASSED 162: VS004: PASSED 162: VS005: PASSED 162: VS006: PASSED 162: VS007: PASSED 162: VS008: PASSED 162: VS009: PASSED 162: VS010: PASSED 162: VS011: PASSED 162: VS012: PASSED 162: VS013: PASSED 162: VS014: PASSED 162: VS015: PASSED 162: VS016: PASSED 162: VS017: PASSED 162: VS018: PASSED 162: VS019: PASSED 162: VS020: PASSED 162: VS021: PASSED 162: VS022: PASSED 162: VS023: PASSED 162: VS024: PASSED 162: VS025: PASSED 162: VS026: PASSED 162: VS027: PASSED 162: VS028: PASSED 162: VS029: PASSED 162: VS030: PASSED 162: VS031: PASSED 162: VS032: PASSED 162: VS033: PASSED 162: VS034: PASSED 162: VS035: PASSED 162: VS036: PASSED 162: VS037: PASSED 162: VS038: PASSED 162: VS039: PASSED 162: VS040: PASSED 162: VS041: PASSED 162: VS042: PASSED 162: VS043: PASSED 162: VS044: PASSED 162: VS045: PASSED 162: VS046: PASSED 162: VS047: PASSED 162: VS048: PASSED 162: VS049: PASSED 162: VS050: PASSED 162: VS051: PASSED 162: VS052: PASSED 162: VS053: PASSED 162: VS054: PASSED 162: VS055: PASSED 162: VS056: PASSED 162: VS057: PASSED 162: VS058: PASSED 162: VS059: PASSED 162: VS060: PASSED 162: VS061: PASSED 162: VS062: PASSED 162: VS063: PASSED 162: VS064: PASSED 162: VS065: PASSED 162: VS066: PASSED 162: VS067: PASSED 162: VS068: PASSED 162: VS069: PASSED 162: VS070: PASSED 162: VS071: PASSED 162: VS072: PASSED 162: VS073: PASSED 162: VS074: PASSED 162: VS075: PASSED 162: VS076: PASSED 162: VS077: PASSED 162: VS078: PASSED 162: VS079: PASSED 162: VS080: PASSED 162: VS081: PASSED 162: VS082: PASSED 162: VS083: PASSED 162: VS084: PASSED 162: VS085: PASSED 162: VS086: PASSED 162: VS087: PASSED 162: VS088: PASSED 162: VS089: PASSED 162: VS090: PASSED 162: VS091: PASSED 162: VS092: PASSED 162: VS093: PASSED 162: VS094: PASSED 162: VS095: PASSED 162: VS096: PASSED 162: VS097: PASSED 162: VS098: PASSED 162: VS099: PASSED 162: VS100: PASSED 162: VS101: PASSED 162: VS102: PASSED 162: VS103: PASSED 162: VS104: PASSED 162: VS105: PASSED 162: VS106: PASSED 162: VS107: PASSED 162: VS108: PASSED 162: VS109: PASSED 162: VS110: PASSED 162: VS111: PASSED 162: VS112: PASSED 162: VS113: PASSED 162: VS114: PASSED 162: VS115: PASSED 162: VS116: PASSED 162: VS117: PASSED 162: VS118: PASSED 162: VS119: PASSED 162: VS120: PASSED 162: VS121: PASSED 162: VS122: PASSED 162: VS123: PASSED 162: VS124: PASSED 162: VS125: PASSED 162: VS126: PASSED 162: VS127: PASSED 162: VS128: PASSED 162: VS129: PASSED 162: VS130: PASSED 162: VS131: PASSED 162: VS132: PASSED 162: VS133: PASSED 162: VS134: PASSED 162: VS135: PASSED 162: VS136: PASSED 162: VS137: PASSED 162: VS138: PASSED 162: VS139: PASSED 162: VS140: PASSED 162: VS141: PASSED 162: VS142: PASSED 162: VS143: PASSED 162: VS144: PASSED 162: VS145: PASSED 162: VS146: PASSED 162: VS147: PASSED 162: VS148: PASSED 162: VS149: PASSED 162: VS150: PASSED 162: VS151: PASSED 162: VS152: PASSED 162: VS153: PASSED 162: VS154: PASSED 162: VS155: PASSED 162: VS156: PASSED 162: VS157: PASSED 162: VS158: PASSED 162: VS159: PASSED 162: VS160: PASSED 162: VS161: PASSED 162: VS162: PASSED 162: VS163: PASSED 162: VS164: PASSED 162: VS165: PASSED 162: VS166: PASSED 162: VS167: PASSED 162: VS168: PASSED 162: VS169: PASSED 162: VS170: PASSED 162: VS171: PASSED 162: VS172: PASSED 162: VS173: PASSED 162: VS174: PASSED 162: VS175: PASSED 162: VS176: PASSED 162: VS177: PASSED 162: VS178: PASSED 162: VS179: PASSED 162: VS180: PASSED 162: VS181: PASSED 162: VS182: PASSED 162: VS183: PASSED 162: VS184: PASSED 162: VS185: PASSED 162: VS186: PASSED 162: VS187: PASSED 162: VS188: PASSED 162: VS189: PASSED 162: VS190: PASSED 162: VS191: PASSED 162: VS192: PASSED 162: VS193: PASSED 162: VS194: PASSED 162: VS195: PASSED 162: VS196: PASSED 162: VS197: PASSED 162: VS198: PASSED 162: VS199: PASSED 162: VS200: PASSED 162: VS201: PASSED 162: VS202: PASSED 162: VS203: PASSED 162: VS204: PASSED 162: VS205: PASSED 162: VS206: PASSED 162: VS207: PASSED 162: VS208: PASSED 162: VS209: PASSED 162: VS210: PASSED 162: VS211: PASSED 162: VS212: PASSED 162: VS213: PASSED 162: VS214: PASSED 162: VS215: PASSED 162: VS216: PASSED 162: VS217: PASSED 162: VS218: PASSED 162: VS219: PASSED 162: VS220: PASSED 162: VS221: PASSED 162: VS222: PASSED 162: VS223: PASSED 162: VS224: PASSED 162: VS225: PASSED 162: VS226: PASSED 162: VS227: PASSED 162: VS228: PASSED 162: VS229: PASSED 162: VS230: PASSED 162: VS231: PASSED 162: VS232: PASSED 162: VS233: PASSED 162: VS234: PASSED 162: VS235: PASSED 162: VS236: PASSED 162: VS237: PASSED 162: VS238: PASSED 162: VS239: PASSED 162: VS240: PASSED 162: VS241: PASSED 162: VS242: PASSED 162: VS243: PASSED 162: VS244: PASSED 162: VS245: PASSED 162: VS246: PASSED 162: VS247: PASSED 162: VS248: PASSED 162: VS249: PASSED 162: VS250: PASSED 162: VS251: PASSED 162: VS252: PASSED 162: VS253: PASSED 162: VS254: PASSED 162: VS255: PASSED 162: VS256: PASSED 162: VS257: PASSED 162: VS258: PASSED 162: VS259: PASSED 162: VS260: PASSED 162: VS261: PASSED 162: VS262: PASSED 162: VS263: PASSED 162: VS264: PASSED 162: VS265: PASSED 162: VS266: PASSED 162: VS267: PASSED 162: VS268: PASSED 162: VS269: PASSED 162: VS270: PASSED 162: VS271: PASSED 162: VS272: PASSED 162: VS273: PASSED 162: VS274: PASSED 162: VS275: PASSED 162: VS276: PASSED 162: VS277: PASSED 162: VS278: PASSED 162: VS279: PASSED 162: VS280: PASSED 162: VS281: PASSED 162: VS282: PASSED 162: VS283: PASSED 162: VS284: PASSED 162: VS285: PASSED 162: VS286: PASSED 162: VS287: PASSED 162: VS288: PASSED 162: VS289: PASSED 162: VS290: PASSED 162: VS291: PASSED 162: VS292: PASSED 162: VS293: PASSED 162: VS294: PASSED 162: VS295: PASSED 162: VS296: PASSED 162: VS297: PASSED 162: VS298: PASSED 162: VS299: PASSED 162: VS300: PASSED 162: Check finished: 0 molecules failed. 162: Failed: 171: Best mapping 203/223 Test #162: pyCIPLabelsValidation .................. Passed 9.24 sec 168: [07:35:08] ------------------------------------- 168: [07:35:08] Results do not depend on numThreads (all same) 204/223 Test #171: testRGroupDecomp ....................... Passed 9.00 sec 168: [07:35:08] ------------------------------------- 168: [07:35:08] testTautomerQueries 168: [07:35:08] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... 168: [07:35:08] ------------------------------------- 168: [07:35:08] github3881 recursive smarts with rings 205/223 Test #168: substructLibraryTest ................... Passed 9.18 sec 170: ......[07:35:08] 170: 170: **** 170: Pre-condition Violation 170: RingInfo not initialized 170: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp 170: Failed Expression: df_init 170: **** 170: 170: [07:35:08] 170: 170: **** 170: Pre-condition Violation 170: RingInfo not initialized 170: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp 170: Failed Expression: df_init 170: **** 170: 223: ................................... 223: ---------------------------------------------------------------------- 223: Ran 35 tests in 1.062s 223: 223: OK 26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import TreeUtils 217: . 217: ---------------------------------------------------------------------- 217: Ran 1 test in 0.000s 217: 217: OK 26: All 191 tests passed 135: ..[07:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTree.py:13: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import Tree 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.012s 223: 223: OK 217: ...... 217: ---------------------------------------------------------------------- 217: Ran 6 tests in 0.001s 217: 217: OK 26: 26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestXVal.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import CrossValidate, randomtest 84: 0,0 0 84: 0,1 0 84: 1,0 0 84: 1,1 0 84: 2,0 0 84: 2,1 0 206/223 Test #84: testEnumeration ........................ Passed 11.09 sec 223: . 223: ---------------------------------------------------------------------- 223: Ran 1 test in 0.009s 223: 223: OK 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.252s 217: 217: OK 223: ....... 223: ---------------------------------------------------------------------- 223: Ran 7 tests in 0.029s 223: 223: OK 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import ID3 217: ...... 217: ---------------------------------------------------------------------- 217: Ran 6 tests in 0.012s 217: 217: OK 139: .............[07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.031s 223: 223: OK 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() 217: .. 217: ---------------------------------------------------------------------- 217: Ran 2 tests in 0.067s 217: 217: OK 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestQuantTree.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import BuildQuantTree 217: .......... 217: ---------------------------------------------------------------------- 217: Ran 10 tests in 0.007s 217: 217: OK 157: Randomness seeded to: 1495546223 157: Timed out after 11 seconds. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestSigTree.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 0.040s 217: 217: OK 215: [07:35:09] INFO: Finished. 215: 217: .. 217: ---------------------------------------------------------------------- 217: Ran 2 tests in 0.002s 217: 217: OK 215: .[07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 0.007s 217: 217: OK 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 170: ............. 170: ---------------------------------------------------------------------- 170: Ran 19 tests in 10.958s 170: 170: OK 170: Testing atom rings 170: testing bond rings 170: searching atom rings 170: searching bond rings 170: done 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: ... 217: ---------------------------------------------------------------------- 217: Ran 3 tests in 0.007s 217: 217: OK 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 207/223 Test #170: pySubstructLibrary ..................... Passed 11.41 sec 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: .ss.ss....... 223: ---------------------------------------------------------------------- 223: Ran 13 tests in 1.010s 223: 223: OK (skipped=4) 217: ... 217: ---------------------------------------------------------------------- 217: Ran 3 tests in 0.181s 217: 217: OK 223: [07:35:10] Molecule does not have explicit Hs. Consider calling AddHs() 223: .[07:35:10] Molecule does not have explicit Hs. Consider calling AddHs() 215: .[07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, 1: terminate called after throwing an instance of 'Invar::Invariant' 1: what(): Expression Failed: 208/223 Test #1: testInchi ..............................Subprocess aborted***Exception: 13.78 sec [07:34:57] ------------------------------------- [07:34:57] ------------------------------------- [07:34:57] ------------------------------------- [07:34:57] ------------------------------------- [07:34:57] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored [07:34:57] ------------------------------------- [07:34:57] ------------------------------------- [07:34:57] ------------------------------------- [07:34:57] Test multithreading reading molecules generating reference data processing launch :0 launch :1 launch :2 launch :3 [07:34:57] **** Test Assert Expression Failed: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp Failed Expression: inchi == inchis[i] **** [07:34:57] Invalid InChI prefix in generating InChI Key [07:34:57] **** Test Assert Expression Failed: Violation occurred on line 45 in file ./External/INCHI-API/test.cpp Failed Expression: key2 == keys[i] **** [07:34:57] **** Test Assert Expression Failed: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp Failed Expression: inchi == inchis[i] **** terminate called after throwing an instance of 'Invar::Invariant' what(): Expression Failed: 217: ...... 217: ---------------------------------------------------------------------- 217: Ran 6 tests in 0.172s 217: 217: OK 215: .[07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 139: ...[07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.Composite import Composite 139: [07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() 139: [07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.ModelPackage import Packager, PackageUtils 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:72: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: model = pickle.load(modelF) 26: All 191 tests passed 26: done 26: ------------------------------------- 26: Unit tests for all MMFF constraint terms. 26: 10.0003 26: done 26: ------------------------------------- 26: Unit test for MMFF TorsionConstraint close to 0 degrees. 26: done 26: ------------------------------------- 26: Unit tests for copying MMFF ForceFields. 26: done 26: ------------------------------------- 26: Unit test for MMFF butane scan. 180: ..[07:35:11] 180: 180: **** 180: Pre-condition Violation 180: no owner 180: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 180: Failed Expression: dp_mol 180: **** 180: 180: [07:35:11] 180: 180: **** 180: Pre-condition Violation 180: no owner 180: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 180: Failed Expression: dp_mol 180: **** 180: 180: [07:35:11] 180: 180: **** 180: Pre-condition Violation 180: no owner 180: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 180: Failed Expression: dp_mol 180: **** 180: 180: [07:35:11] 180: 180: **** 180: Pre-condition Violation 180: no owner 180: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 180: Failed Expression: dp_mol 180: **** 180: 180: [07:35:11] 180: 180: **** 180: Pre-condition Violation 180: no owner 180: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 180: Failed Expression: dp_mol 180: **** 180: 139: ... 139: ---------------------------------------------------------------------- 139: Ran 19 tests in 13.088s 139: 139: OK 139: Testing MolAlign Wrappers 180: .....[07:35:11] 180: 180: **** 180: Range Error 180: atomIdx1 180: Violation occurred on line 377 in file ./Code/GraphMol/RWMol.cpp 180: Failed Expression: 0 < 0 180: **** 180: 217: ....... 217: ---------------------------------------------------------------------- 217: Ran 7 tests in 0.079s 217: 217: OK 180: ......[07:35:11] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 180: [07:35:11] ERROR: Smiles parse error on line 0 180: [07:35:11] ERROR: Cannot create molecule from : 'c1ccccc' 180: [07:35:11] SMILES Parse Error: extra open parentheses for input: 'C(C' 180: [07:35:11] ERROR: Smiles parse error on line 3 180: [07:35:11] ERROR: Cannot create molecule from : 'C(C' 180: [07:35:11] Explicit valence for atom # 1 C, 5, is greater than permitted 180: [07:35:11] ERROR: Could not sanitize molecule on line 6 180: [07:35:11] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 180: [07:35:11] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 180: [07:35:11] ERROR: Smiles parse error on line 0 180: [07:35:11] ERROR: Cannot create molecule from : 'c1ccccc' 180: [07:35:11] SMILES Parse Error: extra open parentheses for input: 'C(C' 180: [07:35:11] ERROR: Smiles parse error on line 3 180: [07:35:11] ERROR: Cannot create molecule from : 'C(C' 180: [07:35:11] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' 180: [07:35:11] ERROR: Smiles parse error on line 6 180: [07:35:11] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' 180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] ERROR: Could not sanitize molecule ending on line 21 180: [07:35:11] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] ERROR: EOF hit while reading atoms 180: [07:35:11] ERROR: moving to the beginning of the next molecule 180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] ERROR: Could not sanitize molecule ending on line 21 180: [07:35:11] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] ERROR: EOF hit while reading atoms 180: [07:35:11] ERROR: moving to the beginning of the next molecule 180: ....[07:35:11] 180: 180: **** 180: Pre-condition Violation 180: RingInfo not initialized 180: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp 180: Failed Expression: df_init 180: **** 180: 180: ..........[07:35:11] 180: 180: **** 180: Range Error 180: idx 180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp 180: Failed Expression: 3 < 1 180: **** 180: 180: ..[07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 209/223 Test #139: pyMolAlign ............................. Passed 13.46 sec 180: ..........................[07:35:11] SMILES Parse Error: unclosed ring for input: 'C1CC' 180: ......[07:35:11] WARNING: not removing hydrogen atom without neighbors 180: [07:35:11] WARNING: not removing hydrogen atom with dummy atom neighbors 180: [07:35:11] WARNING: not removing hydrogen atom with wedged bond 180: [07:35:11] WARNING: not removing hydrogen atom without neighbors 180: [07:35:11] WARNING: not removing hydrogen atom with dummy atom neighbors 26: done 210/223 Test #26: testMMFFForceField ..................... Passed 14.49 sec 180: .....[07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 180: .[07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 180: [07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 180: [07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/NaiveBayes/UnitTestNB.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.NaiveBayes import CrossValidate 180: ..........[07:35:11] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 180: [07:35:11] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 180: .[07:35:11] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 180: [07:35:11] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 180: ..[07:35:11] SMILES Parse Error: syntax error while parsing: error 180: [07:35:11] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' 180: [07:35:11] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' 180: [07:35:11] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' 180: [07:35:11] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.006s 217: 217: OK 180: ................[07:35:12] SMILES Parse Error: syntax error while parsing: garbage_0 180: [07:35:12] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' 180: [07:35:12] SMILES Parse Error: syntax error while parsing: garbage_2 180: [07:35:12] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' 180: [07:35:12] SMILES Parse Error: syntax error while parsing: garbage_4 180: [07:35:12] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 180: .......... 180: ---------------------------------------------------------------------- 180: Ran 248 tests in 11.711s 180: 180: OK 180: 643 180: supplier: 180: supplier: 180: supplier: 211/223 Test #180: pyGraphMolWrap ......................... Passed 12.51 sec 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestTrainer.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.Neural import Network, Trainers 137: --------------------------------- 137: test O3A multithreading bug 137: 137: --------------------------------- 137: testCrippenO3A multithreading 137: 137: generating reference data 215: ....[07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 1.062s 217: 217: OK 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 137: processing 137: launch :0 137: launch :1 137: launch :2 137: launch :3 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestOther.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.001s 217: 217: OK 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.000s 217: 217: OK 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 150: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 150: TOTAL Time elapsed 15.29 seconds 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 212/223 Test #150: testFMCS ............................... Passed 15.33 sec 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.003s 217: 217: OK 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 213/223 Test #217: pythonTestDirML ........................ Passed 11.97 sec 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: .[07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: .[07:35:15] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:15] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:15] INFO: Processing 10 molecules 215: 215: [07:35:15] INFO: Generating fingerprints and descriptors: 215: 215: [07:35:15] INFO: Finished. 215: 215: [07:35:15] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:15] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:15] INFO: Processing 10 molecules 215: 215: [07:35:15] INFO: Generating fingerprints and descriptors: 215: 215: [07:35:15] INFO: Finished. 215: 135: ......[07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: .[07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: .[07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() 135: . 135: ---------------------------------------------------------------------- 135: Ran 19 tests in 17.784s 135: 135: OK 214/223 Test #135: pyDistGeomHelpers ...................... Passed 18.17 sec 215: [07:35:16] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:16] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:16] INFO: Processing 10 molecules 215: 215: [07:35:16] INFO: Generating fingerprints and descriptors: 215: 215: [07:35:16] INFO: Finished. 215: 215: [07:35:17] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:17] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:17] INFO: Generating fingerprints and descriptors: 215: 215: [07:35:17] INFO: Finished. 215: 215: [07:35:17] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:17] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:17] INFO: Generating fingerprints and descriptors: 215: 215: [07:35:17] INFO: Finished. 215: 215: .[07:35:18] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 215: 215: [07:35:18] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:18] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:18] INFO: Processing 163 molecules 215: 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] INFO: done 100 215: 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] INFO: Generating fingerprints and descriptors: 215: 215: [07:35:18] INFO: Finished. 215: 30: [07:35:18] Finished 30: [07:35:18] ------------------------------------- 30: [07:35:18] Test github1843: RWMol.clear() should not destroy ring pointer. 30: [07:35:18] Finished 215/223 Test #30: graphmolTest1 .......................... Passed 21.46 sec 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 6: [07:35:19] Finished: testMultipleTimes() 6: [07:35:19] 6: ----------------------------------------- 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216/223 Test #6: testConcurrentQueue .................... Passed 21.69 sec 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 137: --------------------------------- 137: test getO3AForProbeConfs 137: 137: *********************************************************** 217/223 Test #137: testO3AAlign ........................... Passed 21.12 sec 215: .[07:35:19] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:19] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:19] INFO: Processing 10 molecules 215: 215: [07:35:19] INFO: Generating fingerprints and descriptors: 215: 215: [07:35:19] INFO: Finished. 215: 215: [07:35:20] INFO: Reading molecules and constructing molecular database. 215: 215: [07:35:20] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [07:35:20] INFO: Processing 10 molecules 215: 215: [07:35:21] INFO: Generating fingerprints and descriptors: 215: 215: [07:35:21] INFO: Finished. 215: 215: . 215: ---------------------------------------------------------------------- 215: Ran 12 tests in 19.424s 215: 215: OK 218/223 Test #215: pythonTestDbCLI ........................ Passed 19.77 sec 134: [07:35:34] UFFTYPER: Unrecognized atom type: S_6+6 (0) 134: [07:35:34] UFFTYPER: Warning: hybridization set to SP3 for atom 0 134: [07:35:34] UFFTYPER: Unrecognized charge state for atom: 0 134: =============================================================================== 134: All tests passed (448 assertions in 10 test cases) 134: 219/223 Test #134: distGeomHelpersCatch ................... Passed 36.55 sec 223: ....................[07:35:37] WARNING: More than one matching pattern found - picking one 223: 223: [07:35:37] WARNING: More than one matching pattern found - picking one 223: 223: .[07:35:37] WARNING: More than one matching pattern found - picking one 223: 158: =============================================================================== 158: All tests passed (93 assertions in 5 test cases) 158: 220/223 Test #158: testRascalCluster ...................... Passed 40.50 sec 223: ... 223: ---------------------------------------------------------------------- 223: Ran 25 tests in 30.624s 223: 223: OK 223: {'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl'} 223: {'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl'} 223: {'F[C@H](Cl)[C@@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} 223: !!!! ['C[C@H]([C@H](C)Br)[C@@H](C)F', 'C[C@@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)Br)[C@@H](C)F', 'C[C@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)F)[C@H](C)Br', 'C[C@@H]([C@H](C)F)[C@@H](C)Br', 'C[C@H]([C@H](C)F)[C@H](C)Br', 'C[C@H]([C@H](C)F)[C@@H](C)Br'] 223: ........ 223: ---------------------------------------------------------------------- 223: Ran 8 tests in 0.136s 223: 223: OK 223: .[07:35:42] Molecule does not have explicit Hs. Consider calling AddHs() 223: .....[07:35:46] WARNING: not removing hydrogen atom without neighbors 223: [07:35:46] WARNING: not removing hydrogen atom without neighbors 223: [07:35:46] WARNING: not removing hydrogen atom without neighbors 223: ....[07:35:46] WARNING: not removing hydrogen atom without neighbors 223: ...... 223: ---------------------------------------------------------------------- 223: Ran 16 tests in 3.589s 223: 223: OK 223: [07:35:46] WARNING: Omitted undefined stereo 223: 223: [07:35:46] WARNING: Proton(s) added/removed 223: 223: ..[07:35:48] ERROR: Add/Remove protons error; *Conversion failed* 223: 223: [07:35:48] ERROR: Add/Remove protons error; *Conversion failed* 223: 223: E.... 223: ====================================================================== 223: ERROR: test1InchiReadPubChem (__main__.TestCase.test1InchiReadPubChem) 223: ---------------------------------------------------------------------- 223: Traceback (most recent call last): 223: File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestInchi.py", line 213, in test1InchiReadPubChem 223: for a in unsanitizedInchiMol.GetAtoms() if a.GetNumRadicalElectrons() != 0 223: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 223: AttributeError: 'NoneType' object has no attribute 'GetAtoms' 223: 223: ---------------------------------------------------------------------- 223: Ran 7 tests in 2.440s 223: 223: FAILED (errors=1) 223: 223: InChI write Summary: 1160 identical, 0 suffix variance, 21 reasonable 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 1.448s 223: 223: OK 223: ...... 223: ---------------------------------------------------------------------- 223: Ran 6 tests in 0.347s 223: 223: OK 223: /build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py:218: SyntaxWarning: invalid escape sequence '\O' 223: csv_data = '''"Molecule ChEMBL ID";"Molecule Name";"Molecule Max Phase";"Molecular Weight";"#RO5 Violations";"AlogP";"Compound Key";"Smiles";"Standard Type";"Standard Relation";"Standard Value";"Standard Units";"pChEMBL Value";"Data Validity Comment";"Comment";"Uo Units";"Ligand Efficiency BEI";"Ligand Efficiency LE";"Ligand Efficiency LLE";"Ligand Efficiency SEI";"Potential Duplicate";"Assay ChEMBL ID";"Assay Description";"Assay Type";"BAO Format ID";"BAO Label";"Assay Organism";"Assay Tissue ChEMBL ID";"Assay Tissue Name";"Assay Cell Type";"Assay Subcellular Fraction";"Target ChEMBL ID";"Target Name";"Target Organism";"Target Type";"Document ChEMBL ID";"Source ID";"Source Description";"Document Journal";"Document Year";"Cell ChEMBL ID" 223: Failed to find the pandas get_adjustment() function to patch 223: Failed to patch pandas - PandasTools will have limited functionality 223: Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: FFailed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 133: [07:35:53] done 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: FFailed to patch pandas - unable to change molecule rendering 223: .sFailed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .sFailed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: . 223: ====================================================================== 223: FAIL: testPandasShouldShowMoleculesWhenTruncating (__main__.TestPandasTools.testPandasShouldShowMoleculesWhenTruncating) 223: ---------------------------------------------------------------------- 223: Traceback (most recent call last): 223: File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py", line 229, in testPandasShouldShowMoleculesWhenTruncating 223: self.assertIn('data-content="rdkit/molecule"', html_output) 223: AssertionError: 'data-content="rdkit/molecule"' not found in '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
Molecule ChEMBL IDMolecule NameMolecule Max PhaseMolecular Weight#RO5 Violations...Source DescriptionDocument JournalDocument YearCell ChEMBL IDROMol
0"CHEMBL543779"NaN0341.860...Scientific LiteratureJ. Med. Chem.1986NaN<rdkit.Chem.rdchem.Mol object at 0x7f875127b060>
\n
' 223: 223: ====================================================================== 223: FAIL: test_RestoreMonkeyPatch (__main__.TestPandasTools.test_RestoreMonkeyPatch) 223: ---------------------------------------------------------------------- 223: Traceback (most recent call last): 223: File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py", line 64, in test_RestoreMonkeyPatch 223: self.assertIn('data:image/png;base64', html) 223: AssertionError: 'data:image/png;base64' not found in '\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
prop1prop2IDROMolprop3
012.34qweMethane<rdkit.Chem.rdchem.Mol object at 0x7f875127a180>NaN
1NaNrtzPeroxide<rdkit.Chem.rdchem.Mol object at 0x7f87508ba1f0>yxcv
' 223: 223: ---------------------------------------------------------------------- 223: Ran 28 tests in 1.100s 223: 223: FAILED (failures=2, skipped=2) 133: CNC[C@H]1CC[C@H](C[NH3+])CC1 133: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 133: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 133: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 133: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 133: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 133: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 133: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 133: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 133: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 223: ..............[07:36:03] WARNING: More than one matching pattern found - picking one 223: 223: [07:36:03] WARNING: More than one matching pattern found - picking one 223: 223: ..[07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() 223: [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() 223: [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() 223: [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() 223: ......... 223: ---------------------------------------------------------------------- 223: Ran 25 tests in 9.426s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.054s 223: 223: OK 133: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 157: =============================================================================== 157: All tests passed (2552 assertions in 23 test cases) 157: 221/223 Test #157: testRascalMCES ......................... Passed 65.85 sec 223: ..s... 223: ---------------------------------------------------------------------- 223: Ran 6 tests in 1.017s 223: 223: OK (skipped=1) 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.017s 223: 223: OK 133: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 133: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 133: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 133: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 133: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 133: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 223: .............. 223: ---------------------------------------------------------------------- 223: Ran 14 tests in 2.605s 223: 223: OK 133: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 133: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 133: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 133: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 133: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 133: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 133: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 133: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 133: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 133: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 223: ..[07:36:18] WARNING: not removing hydrogen atom without neighbors 223: .[07:36:18] WARNING: not removing hydrogen atom without neighbors 223: .[07:36:18] WARNING: no name column found on line 1 223: [07:36:18] WARNING: no name column found on line 2 223: [07:36:18] WARNING: no name column found on line 3 223: [07:36:18] WARNING: no name column found on line 4 223: [07:36:18] WARNING: no name column found on line 5 223: [07:36:18] WARNING: no name column found on line 6 223: [07:36:18] WARNING: no name column found on line 7 223: [07:36:18] WARNING: no name column found on line 8 223: [07:36:18] WARNING: no name column found on line 9 223: [07:36:18] WARNING: no name column found on line 10 223: [07:36:18] WARNING: no name column found on line 11 223: [07:36:18] WARNING: no name column found on line 12 223: [07:36:18] WARNING: no name column found on line 13 223: [07:36:18] WARNING: no name column found on line 14 223: [07:36:18] WARNING: no name column found on line 15 223: [07:36:18] WARNING: no name column found on line 16 223: [07:36:18] WARNING: no name column found on line 17 223: [07:36:18] WARNING: no name column found on line 18 223: [07:36:18] WARNING: no name column found on line 19 223: [07:36:18] WARNING: no name column found on line 20 223: [07:36:18] WARNING: no name column found on line 21 223: [07:36:18] WARNING: no name column found on line 22 223: [07:36:18] WARNING: no name column found on line 23 223: [07:36:18] WARNING: no name column found on line 24 223: [07:36:18] WARNING: no name column found on line 25 223: [07:36:18] WARNING: no name column found on line 26 223: [07:36:18] WARNING: no name column found on line 27 223: [07:36:18] WARNING: no name column found on line 28 223: [07:36:18] WARNING: no name column found on line 29 223: [07:36:18] WARNING: no name column found on line 30 223: [07:36:18] WARNING: no name column found on line 31 223: [07:36:18] WARNING: no name column found on line 32 223: [07:36:18] WARNING: no name column found on line 33 223: [07:36:18] WARNING: no name column found on line 34 223: [07:36:18] WARNING: no name column found on line 35 223: [07:36:18] WARNING: no name column found on line 36 223: [07:36:18] WARNING: no name column found on line 37 223: [07:36:18] WARNING: no name column found on line 38 223: [07:36:18] WARNING: no name column found on line 39 223: [07:36:18] WARNING: no name column found on line 40 223: [07:36:18] WARNING: no name column found on line 41 223: [07:36:18] WARNING: no name column found on line 42 223: [07:36:18] WARNING: no name column found on line 43 223: [07:36:18] WARNING: no name column found on line 44 223: [07:36:18] WARNING: no name column found on line 45 223: [07:36:18] WARNING: no name column found on line 46 223: [07:36:18] WARNING: no name column found on line 47 223: [07:36:18] WARNING: no name column found on line 48 223: [07:36:18] WARNING: no name column found on line 49 223: [07:36:18] WARNING: no name column found on line 50 223: [07:36:18] WARNING: no name column found on line 51 223: [07:36:18] WARNING: no name column found on line 52 223: [07:36:18] WARNING: no name column found on line 53 223: [07:36:18] WARNING: no name column found on line 54 223: [07:36:18] WARNING: no name column found on line 55 223: [07:36:18] WARNING: no name column found on line 56 223: [07:36:18] WARNING: no name column found on line 57 223: [07:36:18] WARNING: no name column found on line 58 223: [07:36:18] WARNING: no name column found on line 59 223: [07:36:18] WARNING: no name column found on line 60 223: [07:36:18] WARNING: no name column found on line 61 223: [07:36:18] WARNING: no name column found on line 62 223: [07:36:18] WARNING: no name column found on line 63 223: [07:36:18] WARNING: no name column found on line 64 223: [07:36:18] WARNING: no name column found on line 65 223: [07:36:18] WARNING: no name column found on line 66 223: [07:36:18] WARNING: no name column found on line 67 223: [07:36:18] WARNING: no name column found on line 68 223: [07:36:18] WARNING: no name column found on line 69 223: [07:36:18] WARNING: no name column found on line 70 223: [07:36:18] WARNING: no name column found on line 71 223: [07:36:18] WARNING: no name column found on line 72 223: [07:36:18] WARNING: no name column found on line 73 223: [07:36:18] WARNING: no name column found on line 74 223: [07:36:18] WARNING: no name column found on line 75 223: [07:36:18] WARNING: no name column found on line 76 223: [07:36:18] WARNING: no name column found on line 77 223: [07:36:18] WARNING: no name column found on line 78 223: [07:36:18] WARNING: no name column found on line 79 223: [07:36:18] WARNING: no name column found on line 80 223: [07:36:18] WARNING: no name column found on line 81 223: [07:36:18] WARNING: no name column found on line 82 223: [07:36:18] WARNING: no name column found on line 83 223: [07:36:18] WARNING: no name column found on line 84 223: [07:36:18] WARNING: no name column found on line 85 223: [07:36:18] WARNING: no name column found on line 86 223: [07:36:18] WARNING: no name column found on line 87 223: [07:36:18] WARNING: no name column found on line 88 223: [07:36:18] WARNING: no name column found on line 89 223: [07:36:18] WARNING: no name column found on line 90 223: [07:36:18] WARNING: no name column found on line 91 223: [07:36:18] WARNING: no name column found on line 92 223: [07:36:18] WARNING: no name column found on line 93 223: [07:36:18] WARNING: no name column found on line 94 223: [07:36:18] WARNING: no name column found on line 95 223: [07:36:18] WARNING: no name column found on line 96 223: [07:36:18] WARNING: no name column found on line 97 223: [07:36:18] WARNING: no name column found on line 98 223: [07:36:18] WARNING: no name column found on line 99 223: [07:36:18] WARNING: no name column found on line 100 223: [07:36:18] WARNING: no name column found on line 101 223: [07:36:18] WARNING: no name column found on line 102 223: [07:36:18] WARNING: no name column found on line 103 223: [07:36:18] WARNING: no name column found on line 104 223: [07:36:18] WARNING: no name column found on line 105 223: [07:36:18] WARNING: no name column found on line 106 223: [07:36:18] WARNING: no name column found on line 107 223: [07:36:18] WARNING: no name column found on line 108 223: [07:36:18] WARNING: no name column found on line 109 223: [07:36:18] WARNING: no name column found on line 110 223: [07:36:18] WARNING: no name column found on line 111 223: [07:36:18] WARNING: no name column found on line 112 223: [07:36:18] WARNING: no name column found on line 113 223: [07:36:18] WARNING: no name column found on line 114 223: [07:36:18] WARNING: no name column found on line 115 223: [07:36:18] WARNING: no name column found on line 116 223: [07:36:18] WARNING: no name column found on line 117 223: [07:36:18] WARNING: no name column found on line 118 223: [07:36:18] WARNING: no name column found on line 119 223: [07:36:18] WARNING: no name column found on line 120 223: [07:36:18] WARNING: no name column found on line 121 223: [07:36:18] WARNING: no name column found on line 122 223: [07:36:18] WARNING: no name column found on line 123 223: [07:36:18] WARNING: no name column found on line 124 223: [07:36:18] WARNING: no name column found on line 125 223: [07:36:18] WARNING: no name column found on line 126 223: [07:36:18] WARNING: no name column found on line 127 223: [07:36:18] WARNING: no name column found on line 128 223: [07:36:18] WARNING: no name column found on line 129 223: [07:36:18] WARNING: no name column found on line 130 223: [07:36:18] WARNING: no name column found on line 131 223: [07:36:18] WARNING: no name column found on line 132 223: [07:36:18] WARNING: no name column found on line 133 223: [07:36:18] WARNING: no name column found on line 134 223: [07:36:18] WARNING: no name column found on line 135 223: [07:36:18] WARNING: no name column found on line 136 223: [07:36:18] WARNING: no name column found on line 137 223: [07:36:18] WARNING: no name column found on line 138 223: [07:36:18] WARNING: no name column found on line 139 223: [07:36:18] WARNING: no name column found on line 140 223: [07:36:18] WARNING: no name column found on line 141 223: [07:36:18] WARNING: no name column found on line 142 223: [07:36:18] WARNING: no name column found on line 143 223: [07:36:18] WARNING: no name column found on line 144 223: [07:36:18] WARNING: no name column found on line 145 223: [07:36:18] WARNING: no name column found on line 146 223: [07:36:18] WARNING: no name column found on line 147 223: [07:36:18] WARNING: no name column found on line 148 223: [07:36:18] WARNING: no name column found on line 149 223: [07:36:18] WARNING: no name column found on line 150 223: [07:36:18] WARNING: no name column found on line 151 223: [07:36:18] WARNING: no name column found on line 152 223: [07:36:18] WARNING: no name column found on line 153 223: [07:36:18] WARNING: no name column found on line 154 223: [07:36:18] WARNING: no name column found on line 155 223: [07:36:18] WARNING: no name column found on line 156 223: [07:36:18] WARNING: no name column found on line 157 223: [07:36:18] WARNING: no name column found on line 158 223: [07:36:18] WARNING: no name column found on line 159 223: [07:36:18] WARNING: no name column found on line 160 223: [07:36:18] WARNING: no name column found on line 161 223: [07:36:18] WARNING: no name column found on line 162 223: [07:36:18] WARNING: no name column found on line 163 223: [07:36:18] WARNING: no name column found on line 164 223: [07:36:18] WARNING: no name column found on line 165 223: [07:36:18] WARNING: no name column found on line 166 223: [07:36:18] WARNING: no name column found on line 167 223: [07:36:18] WARNING: no name column found on line 168 223: [07:36:18] WARNING: no name column found on line 169 223: [07:36:18] WARNING: no name column found on line 170 223: [07:36:18] WARNING: no name column found on line 171 223: [07:36:18] WARNING: no name column found on line 172 223: [07:36:18] WARNING: no name column found on line 173 223: [07:36:18] WARNING: no name column found on line 174 223: [07:36:18] WARNING: no name column found on line 175 223: [07:36:18] WARNING: no name column found on line 176 223: [07:36:18] WARNING: no name column found on line 177 223: [07:36:18] WARNING: no name column found on line 178 223: [07:36:18] WARNING: no name column found on line 179 223: [07:36:18] WARNING: no name column found on line 180 223: [07:36:18] WARNING: no name column found on line 181 223: [07:36:18] WARNING: no name column found on line 182 223: [07:36:18] WARNING: no name column found on line 183 223: [07:36:18] WARNING: no name column found on line 184 223: [07:36:18] WARNING: no name column found on line 185 223: [07:36:18] WARNING: no name column found on line 186 223: [07:36:18] WARNING: no name column found on line 187 223: [07:36:18] WARNING: no name column found on line 188 223: [07:36:18] WARNING: no name column found on line 189 223: [07:36:18] WARNING: no name column found on line 190 223: [07:36:18] WARNING: no name column found on line 191 223: [07:36:18] WARNING: no name column found on line 192 223: [07:36:18] WARNING: no name column found on line 193 223: [07:36:18] WARNING: no name column found on line 194 223: [07:36:18] WARNING: no name column found on line 195 223: [07:36:18] WARNING: no name column found on line 196 223: [07:36:18] WARNING: no name column found on line 197 223: [07:36:18] WARNING: no name column found on line 198 223: [07:36:18] WARNING: no name column found on line 199 223: [07:36:18] WARNING: no name column found on line 200 223: [07:36:18] WARNING: no name column found on line 201 223: [07:36:18] WARNING: no name column found on line 202 223: [07:36:18] WARNING: no name column found on line 203 223: [07:36:18] WARNING: no name column found on line 204 223: [07:36:18] WARNING: no name column found on line 205 223: [07:36:18] WARNING: no name column found on line 206 223: [07:36:18] WARNING: no name column found on line 207 223: [07:36:18] WARNING: no name column found on line 208 223: [07:36:18] WARNING: no name column found on line 209 223: [07:36:18] WARNING: no name column found on line 210 223: [07:36:18] WARNING: no name column found on line 211 223: [07:36:18] WARNING: no name column found on line 212 223: [07:36:18] WARNING: no name column found on line 213 223: [07:36:18] WARNING: no name column found on line 214 223: [07:36:18] WARNING: no name column found on line 215 223: [07:36:18] WARNING: no name column found on line 216 223: ...... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.162s 223: 223: OK 133: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 133: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] 223: .................. 223: ---------------------------------------------------------------------- 223: Ran 18 tests in 0.901s 223: 223: OK 133: [07:36:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 133: [07:36:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.068s 223: 223: OK 223: ........ 223: ---------------------------------------------------------------------- 223: Ran 8 tests in 0.029s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.015s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.017s 223: 223: OK 223: . 223: ---------------------------------------------------------------------- 223: Ran 1 test in 0.088s 223: 223: OK 223: ........ 223: ---------------------------------------------------------------------- 223: Ran 8 tests in 0.002s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.006s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.002s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.005s 223: 223: OK 223: ....... 223: ---------------------------------------------------------------------- 223: Ran 7 tests in 0.014s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.021s 223: 223: OK 133: [07:36:29] Molecule does not have explicit Hs. Consider calling AddHs() 222/223 Test #133: testDistGeomHelpers .................... Passed 90.96 sec 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 3.014s 223: 223: OK 223: .......... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.052s 223: 223: OK 223: . 223: ---------------------------------------------------------------------- 223: Ran 1 test in 0.000s 223: 223: OK 223: .......... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.006s 223: 223: OK 223: ..... 223: ---------------------------------------------------------------------- 223: Ran 5 tests in 0.078s 223: 223: OK 223: .........[07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: .......[07:36:36] Molecule does not have explicit Hs. Consider calling AddHs() 223: [07:36:36] Molecule does not have explicit Hs. Consider calling AddHs() 223: ..... 223: ---------------------------------------------------------------------- 223: Ran 21 tests in 5.392s 223: 223: OK 223: mol_197 223: 219.10,35.89,110.98,11.56,110.32,11.04,95.23,10.25,0.00 223: mol_223 223: 243.67,7.40,134.64,0.81,134.56,0.81,85.50,0.37,0.00 223: mol_269 223: 216.26,5.67,105.00,0.87,103.81,0.89,89.27,0.92,6.00 223: . 223: ---------------------------------------------------------------------- 223: Ran 1 test in 0.000s 223: 223: OK 223: ...[07:36:37] 223: 223: **** 223: Pre-condition Violation 223: molecule has no conformers 223: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 223: Failed Expression: dp_mol->getNumConformers() 223: **** 223: 223: . 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.013s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 6.519s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.111s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.014s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.021s 223: 223: OK 223: .....[07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: [07:36:46] WARNING: not removing hydrogen atom without neighbors 223: ..... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.350s 223: 223: OK 223: ssssss..........s/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually 223: warnings.warn( 223: ..... 223: ---------------------------------------------------------------------- 223: Ran 22 tests in 4.573s 223: 223: OK (skipped=7) 223: sss. 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.522s 223: 223: OK (skipped=3) 223: ssss 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.000s 223: 223: OK (skipped=4) 223: .......... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.827s 223: 223: OK 223: ...[07:36:55] SMARTS Parse Error: syntax error while parsing: boromicacid 223: [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 223: [07:36:55] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 223: [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 223: [07:36:55] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 223: [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 223: [07:36:55] reaction has no reactants 223: [07:36:55] reaction has no products 223: [07:36:55] initialization failed 223: [07:36:55] reaction has no reactants 223: [07:36:55] reaction has no products 223: . 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.026s 223: 223: OK 223: ['C[C@@H](F)CN', 'C[C@@H](F)CN |a:1|', 'C[C@H](F)CN |o1:1|', 'C[C@H](F)CN |&1:1|'] 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.011s 223: 223: OK 223: ........................ 223: ---------------------------------------------------------------------- 223: Ran 24 tests in 0.095s 223: 223: OK 223: !!! TEST FAILURE: python UnitTestInchi.py {} 223: !!! TEST FAILURE: python UnitTestPandasTools.py {} 223/223 Test #223: pythonTestDirChem ......................***Failed 114.27 sec ....... ---------------------------------------------------------------------- Ran 7 tests in 0.167s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.047s OK ....[07:35:04] **** Pre-condition Violation valence not defined for atoms not associated with molecules Violation occurred on line 411 in file ./Code/GraphMol/Atom.cpp Failed Expression: dp_mol **** . ---------------------------------------------------------------------- Ran 5 tests in 0.031s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.024s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.012s OK ...................... ---------------------------------------------------------------------- Ran 22 tests in 0.039s OK .....s.................ss ---------------------------------------------------------------------- Ran 25 tests in 0.115s OK (skipped=3) ..s ---------------------------------------------------------------------- Ran 3 tests in 0.143s OK (skipped=1) ................................... ---------------------------------------------------------------------- Ran 35 tests in 1.062s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.012s OK . ---------------------------------------------------------------------- Ran 1 test in 0.009s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.029s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.031s OK .ss.ss....... ---------------------------------------------------------------------- Ran 13 tests in 1.010s OK (skipped=4) [07:35:10] Molecule does not have explicit Hs. Consider calling AddHs() .[07:35:10] Molecule does not have explicit Hs. Consider calling AddHs() ....................[07:35:37] WARNING: More than one matching pattern found - picking one [07:35:37] WARNING: More than one matching pattern found - picking one .[07:35:37] WARNING: More than one matching pattern found - picking one ... ---------------------------------------------------------------------- Ran 25 tests in 30.624s OK {'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl'} {'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl'} {'F[C@H](Cl)[C@@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} !!!! ['C[C@H]([C@H](C)Br)[C@@H](C)F', 'C[C@@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)Br)[C@@H](C)F', 'C[C@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)F)[C@H](C)Br', 'C[C@@H]([C@H](C)F)[C@@H](C)Br', 'C[C@H]([C@H](C)F)[C@H](C)Br', 'C[C@H]([C@H](C)F)[C@@H](C)Br'] ........ ---------------------------------------------------------------------- Ran 8 tests in 0.136s OK .[07:35:42] Molecule does not have explicit Hs. Consider calling AddHs() .....[07:35:46] WARNING: not removing hydrogen atom without neighbors [07:35:46] WARNING: not removing hydrogen atom without neighbors [07:35:46] WARNING: not removing hydrogen atom without neighbors ....[07:35:46] WARNING: not removing hydrogen atom without neighbors ...... ---------------------------------------------------------------------- Ran 16 tests in 3.589s OK [07:35:46] WARNING: Omitted undefined stereo [07:35:46] WARNING: Proton(s) added/removed ..[07:35:48] ERROR: Add/Remove protons error; *Conversion failed* [07:35:48] ERROR: Add/Remove protons error; *Conversion failed* E.... ====================================================================== ERROR: test1InchiReadPubChem (__main__.TestCase.test1InchiReadPubChem) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestInchi.py", line 213, in test1InchiReadPubChem for a in unsanitizedInchiMol.GetAtoms() if a.GetNumRadicalElectrons() != 0 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'GetAtoms' ---------------------------------------------------------------------- Ran 7 tests in 2.440s FAILED (errors=1) InChI write Summary: 1160 identical, 0 suffix variance, 21 reasonable .... ---------------------------------------------------------------------- Ran 4 tests in 1.448s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.347s OK /build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py:218: SyntaxWarning: invalid escape sequence '\O' csv_data = '''"Molecule ChEMBL ID";"Molecule Name";"Molecule Max Phase";"Molecular Weight";"#RO5 Violations";"AlogP";"Compound Key";"Smiles";"Standard Type";"Standard Relation";"Standard Value";"Standard Units";"pChEMBL Value";"Data Validity Comment";"Comment";"Uo Units";"Ligand Efficiency BEI";"Ligand Efficiency LE";"Ligand Efficiency LLE";"Ligand Efficiency SEI";"Potential Duplicate";"Assay ChEMBL ID";"Assay Description";"Assay Type";"BAO Format ID";"BAO Label";"Assay Organism";"Assay Tissue ChEMBL ID";"Assay Tissue Name";"Assay Cell Type";"Assay Subcellular Fraction";"Target ChEMBL ID";"Target Name";"Target Organism";"Target Type";"Document ChEMBL ID";"Source ID";"Source Description";"Document Journal";"Document Year";"Cell ChEMBL ID" Failed to find the pandas get_adjustment() function to patch Failed to patch pandas - PandasTools will have limited functionality Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering FFailed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering Failed to patch pandas - unable to change molecule rendering FFailed to patch pandas - unable to change molecule rendering .sFailed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .sFailed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering .Failed to patch pandas - unable to change molecule rendering . ====================================================================== FAIL: testPandasShouldShowMoleculesWhenTruncating (__main__.TestPandasTools.testPandasShouldShowMoleculesWhenTruncating) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py", line 229, in testPandasShouldShowMoleculesWhenTruncating self.assertIn('data-content="rdkit/molecule"', html_output) AssertionError: 'data-content="rdkit/molecule"' not found in '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
Molecule ChEMBL IDMolecule NameMolecule Max PhaseMolecular Weight#RO5 Violations...Source DescriptionDocument JournalDocument YearCell ChEMBL IDROMol
0"CHEMBL543779"NaN0341.860...Scientific LiteratureJ. Med. Chem.1986NaN<rdkit.Chem.rdchem.Mol object at 0x7f875127b060>
\n
' ====================================================================== FAIL: test_RestoreMonkeyPatch (__main__.TestPandasTools.test_RestoreMonkeyPatch) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py", line 64, in test_RestoreMonkeyPatch self.assertIn('data:image/png;base64', html) AssertionError: 'data:image/png;base64' not found in '\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
prop1prop2IDROMolprop3
012.34qweMethane<rdkit.Chem.rdchem.Mol object at 0x7f875127a180>NaN
1NaNrtzPeroxide<rdkit.Chem.rdchem.Mol object at 0x7f87508ba1f0>yxcv
' ---------------------------------------------------------------------- Ran 28 tests in 1.100s FAILED (failures=2, skipped=2) ..............[07:36:03] WARNING: More than one matching pattern found - picking one [07:36:03] WARNING: More than one matching pattern found - picking one ..[07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() ......... ---------------------------------------------------------------------- Ran 25 tests in 9.426s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.054s OK ..s... ---------------------------------------------------------------------- Ran 6 tests in 1.017s OK (skipped=1) .. ---------------------------------------------------------------------- Ran 2 tests in 0.017s OK .............. ---------------------------------------------------------------------- Ran 14 tests in 2.605s OK ..[07:36:18] WARNING: not removing hydrogen atom without neighbors .[07:36:18] WARNING: not removing hydrogen atom without neighbors .[07:36:18] WARNING: no name column found on line 1 [07:36:18] WARNING: no name column found on line 2 [07:36:18] WARNING: no name column found on line 3 [07:36:18] WARNING: no name column found on line 4 [07:36:18] WARNING: no name column found on line 5 [07:36:18] WARNING: no name column found on line 6 [07:36:18] WARNING: no name column found on line 7 [07:36:18] WARNING: no name column found on line 8 [07:36:18] WARNING: no name column found on line 9 [07:36:18] WARNING: no name column found on line 10 [07:36:18] WARNING: no name column found on line 11 [07:36:18] WARNING: no name column found on line 12 [07:36:18] WARNING: no name column found on line 13 [07:36:18] WARNING: no name column found on line 14 [07:36:18] WARNING: no name column found on line 15 [07:36:18] WARNING: no name column found on line 16 [07:36:18] WARNING: no name column found on line 17 [07:36:18] WARNING: no name column found on line 18 [07:36:18] WARNING: no name column found on line 19 [07:36:18] WARNING: no name column found on line 20 [07:36:18] WARNING: no name column found on line 21 [07:36:18] WARNING: no name column found on line 22 [07:36:18] WARNING: no name column found on line 23 [07:36:18] WARNING: no name column found on line 24 [07:36:18] WARNING: no name column found on line 25 [07:36:18] WARNING: no name column found on line 26 [07:36:18] WARNING: no name column found on line 27 [07:36:18] WARNING: no name column found on line 28 [07:36:18] WARNING: no name column found on line 29 [07:36:18] WARNING: no name column found on line 30 [07:36:18] WARNING: no name column found on line 31 [07:36:18] WARNING: no name column found on line 32 [07:36:18] WARNING: no name column found on line 33 [07:36:18] WARNING: no name column found on line 34 [07:36:18] WARNING: no name column found on line 35 [07:36:18] WARNING: no name column found on line 36 [07:36:18] WARNING: no name column found on line 37 [07:36:18] WARNING: no name column found on line 38 [07:36:18] WARNING: no name column found on line 39 [07:36:18] WARNING: no name column found on line 40 [07:36:18] WARNING: no name column found on line 41 [07:36:18] WARNING: no name column found on line 42 [07:36:18] WARNING: no name column found on line 43 [07:36:18] WARNING: no name column found on line 44 [07:36:18] WARNING: no name column found on line 45 [07:36:18] WARNING: no name column found on line 46 [07:36:18] WARNING: no name column found on line 47 [07:36:18] WARNING: no name column found on line 48 [07:36:18] WARNING: no name column found on line 49 [07:36:18] WARNING: no name column found on line 50 [07:36:18] WARNING: no name column found on line 51 [07:36:18] WARNING: no name column found on line 52 [07:36:18] WARNING: no name column found on line 53 [07:36:18] WARNING: no name column found on line 54 [07:36:18] WARNING: no name column found on line 55 [07:36:18] WARNING: no name column found on line 56 [07:36:18] WARNING: no name column found on line 57 [07:36:18] WARNING: no name column found on line 58 [07:36:18] WARNING: no name column found on line 59 [07:36:18] WARNING: no name column found on line 60 [07:36:18] WARNING: no name column found on line 61 [07:36:18] WARNING: no name column found on line 62 [07:36:18] WARNING: no name column found on line 63 [07:36:18] WARNING: no name column found on line 64 [07:36:18] WARNING: no name column found on line 65 [07:36:18] WARNING: no name column found on line 66 [07:36:18] WARNING: no name column found on line 67 [07:36:18] WARNING: no name column found on line 68 [07:36:18] WARNING: no name column found on line 69 [07:36:18] WARNING: no name column found on line 70 [07:36:18] WARNING: no name column found on line 71 [07:36:18] WARNING: no name column found on line 72 [07:36:18] WARNING: no name column found on line 73 [07:36:18] WARNING: no name column found on line 74 [07:36:18] WARNING: no name column found on line 75 [07:36:18] WARNING: no name column found on line 76 [07:36:18] WARNING: no name column found on line 77 [07:36:18] WARNING: no name column found on line 78 [07:36:18] WARNING: no name column found on line 79 [07:36:18] WARNING: no name column found on line 80 [07:36:18] WARNING: no name column found on line 81 [07:36:18] WARNING: no name column found on line 82 [07:36:18] WARNING: no name column found on 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[07:36:18] WARNING: no name column found on line 103 [07:36:18] WARNING: no name column found on line 104 [07:36:18] WARNING: no name column found on line 105 [07:36:18] WARNING: no name column found on line 106 [07:36:18] WARNING: no name column found on line 107 [07:36:18] WARNING: no name column found on line 108 [07:36:18] WARNING: no name column found on line 109 [07:36:18] WARNING: no name column found on line 110 [07:36:18] WARNING: no name column found on line 111 [07:36:18] WARNING: no name column found on line 112 [07:36:18] WARNING: no name column found on line 113 [07:36:18] WARNING: no name column found on line 114 [07:36:18] WARNING: no name column found on line 115 [07:36:18] WARNING: no name column found on line 116 [07:36:18] WARNING: no name column found on line 117 [07:36:18] WARNING: no name column found on line 118 [07:36:18] WARNING: no name column found on line 119 [07:36:18] WARNING: no name column found on line 120 [07:36:18] WARNING: no name column found on line 121 [07:36:18] WARNING: no name column found on line 122 [07:36:18] WARNING: no name column found on line 123 [07:36:18] WARNING: no name column found on line 124 [07:36:18] WARNING: no name column found on line 125 [07:36:18] WARNING: no name column found on line 126 [07:36:18] WARNING: no name column found on line 127 [07:36:18] WARNING: no name column found on line 128 [07:36:18] WARNING: no name column found on line 129 [07:36:18] WARNING: no name column found on line 130 [07:36:18] WARNING: no name column found on line 131 [07:36:18] WARNING: no name column found on line 132 [07:36:18] WARNING: no name column found on line 133 [07:36:18] WARNING: no name column found on line 134 [07:36:18] WARNING: no name column found on line 135 [07:36:18] WARNING: no name column found on line 136 [07:36:18] WARNING: no name column found on line 137 [07:36:18] WARNING: no name column found on line 138 [07:36:18] WARNING: no name column found on line 139 [07:36:18] WARNING: no name column found on line 140 [07:36:18] WARNING: no name column found on line 141 [07:36:18] WARNING: no name column found on line 142 [07:36:18] WARNING: no name column found on line 143 [07:36:18] WARNING: no name column found on line 144 [07:36:18] WARNING: no name column found on line 145 [07:36:18] WARNING: no name column found on line 146 [07:36:18] WARNING: no name column found on line 147 [07:36:18] WARNING: no name column found on line 148 [07:36:18] WARNING: no name column found on line 149 [07:36:18] WARNING: no name column found on line 150 [07:36:18] WARNING: no name column found on line 151 [07:36:18] WARNING: no name column found on line 152 [07:36:18] WARNING: no name column found on line 153 [07:36:18] WARNING: no name column found on line 154 [07:36:18] WARNING: no name column found on line 155 [07:36:18] WARNING: no name column found on line 156 [07:36:18] WARNING: no name column found on line 157 [07:36:18] WARNING: no name column found on line 158 [07:36:18] WARNING: no name column found on line 159 [07:36:18] WARNING: no name column found on line 160 [07:36:18] WARNING: no name column found on line 161 [07:36:18] WARNING: no name column found on line 162 [07:36:18] WARNING: no name column found on line 163 [07:36:18] WARNING: no name column found on line 164 [07:36:18] WARNING: no name column found on line 165 [07:36:18] WARNING: no name column found on line 166 [07:36:18] WARNING: no name column found on line 167 [07:36:18] WARNING: no name column found on line 168 [07:36:18] WARNING: no name column found on line 169 [07:36:18] WARNING: no name column found on line 170 [07:36:18] WARNING: no name column found on line 171 [07:36:18] WARNING: no name column found on line 172 [07:36:18] WARNING: no name column found on line 173 [07:36:18] WARNING: no name column found on line 174 [07:36:18] WARNING: no name column found on line 175 [07:36:18] WARNING: no name column found on line 176 [07:36:18] WARNING: no name column found on line 177 [07:36:18] WARNING: no name column found on line 178 [07:36:18] WARNING: no name column found on line 179 [07:36:18] WARNING: no name column found on line 180 [07:36:18] WARNING: no name column found on line 181 [07:36:18] WARNING: no name column found on line 182 [07:36:18] WARNING: no name column found on line 183 [07:36:18] WARNING: no name column found on line 184 [07:36:18] WARNING: no name column found on line 185 [07:36:18] WARNING: no name column found on line 186 [07:36:18] WARNING: no name column found on line 187 [07:36:18] WARNING: no name column found on line 188 [07:36:18] WARNING: no name column found on line 189 [07:36:18] WARNING: no name column found on line 190 [07:36:18] WARNING: no name column found on line 191 [07:36:18] WARNING: no name column found on line 192 [07:36:18] WARNING: no name column found on line 193 [07:36:18] WARNING: no name column found on line 194 [07:36:18] WARNING: no name column found on line 195 [07:36:18] WARNING: no name column found on line 196 [07:36:18] WARNING: no name column found on line 197 [07:36:18] WARNING: no name column found on line 198 [07:36:18] WARNING: no name column found on line 199 [07:36:18] WARNING: no name column found on line 200 [07:36:18] WARNING: no name column found on line 201 [07:36:18] WARNING: no name column found on line 202 [07:36:18] WARNING: no name column found on line 203 [07:36:18] WARNING: no name column found on line 204 [07:36:18] WARNING: no name column found on line 205 [07:36:18] WARNING: no name column found on line 206 [07:36:18] WARNING: no name column found on line 207 [07:36:18] WARNING: no name column found on line 208 [07:36:18] WARNING: no name column found on line 209 [07:36:18] WARNING: no name column found on line 210 [07:36:18] WARNING: no name column found on line 211 [07:36:18] WARNING: no name column found on line 212 [07:36:18] WARNING: no name column found on line 213 [07:36:18] WARNING: no name column found on line 214 [07:36:18] WARNING: no name column found on line 215 [07:36:18] WARNING: no name column found on line 216 ...... ---------------------------------------------------------------------- Ran 10 tests in 0.162s OK .................. ---------------------------------------------------------------------- Ran 18 tests in 0.901s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.068s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.029s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.015s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.017s OK . ---------------------------------------------------------------------- Ran 1 test in 0.088s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.002s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.006s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.002s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.005s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.014s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.021s OK .... ---------------------------------------------------------------------- Ran 4 tests in 3.014s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.052s OK . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.006s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 0.078s OK .........[07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. .......[07:36:36] Molecule does not have explicit Hs. Consider calling AddHs() [07:36:36] Molecule does not have explicit Hs. Consider calling AddHs() ..... ---------------------------------------------------------------------- Ran 21 tests in 5.392s OK mol_197 219.10,35.89,110.98,11.56,110.32,11.04,95.23,10.25,0.00 mol_223 243.67,7.40,134.64,0.81,134.56,0.81,85.50,0.37,0.00 mol_269 216.26,5.67,105.00,0.87,103.81,0.89,89.27,0.92,6.00 . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK ...[07:36:37] **** Pre-condition Violation molecule has no conformers Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp Failed Expression: dp_mol->getNumConformers() **** . ---------------------------------------------------------------------- Ran 4 tests in 0.013s OK .. ---------------------------------------------------------------------- Ran 2 tests in 6.519s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.111s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.014s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.021s OK .....[07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors [07:36:46] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- Ran 10 tests in 0.350s OK ssssss..........s/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually warnings.warn( ..... ---------------------------------------------------------------------- Ran 22 tests in 4.573s OK (skipped=7) sss. ---------------------------------------------------------------------- Ran 4 tests in 0.522s OK (skipped=3) ssss ---------------------------------------------------------------------- Ran 4 tests in 0.000s OK (skipped=4) .......... ---------------------------------------------------------------------- Ran 10 tests in 0.827s OK ...[07:36:55] SMARTS Parse Error: syntax error while parsing: boromicacid [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' [07:36:55] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' [07:36:55] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' [07:36:55] reaction has no reactants [07:36:55] reaction has no products [07:36:55] initialization failed [07:36:55] reaction has no reactants [07:36:55] reaction has no products . ---------------------------------------------------------------------- Ran 4 tests in 0.026s OK ['C[C@@H](F)CN', 'C[C@@H](F)CN |a:1|', 'C[C@H](F)CN |o1:1|', 'C[C@H](F)CN |&1:1|'] .... ---------------------------------------------------------------------- Ran 4 tests in 0.011s OK ........................ ---------------------------------------------------------------------- Ran 24 tests in 0.095s OK !!! TEST FAILURE: python UnitTestInchi.py {} !!! TEST FAILURE: python UnitTestPandasTools.py {} 99% tests passed, 3 tests failed out of 223 Total Test time (real) = 119.31 sec The following tests FAILED: 1 - testInchi (Subprocess aborted) 219 - pythonTestDirDbase (Failed) 223 - pythonTestDirChem (Failed) Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 returned exit code 2 make[1]: [debian/rules:134: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' create-stamp debian/debhelper-build-stamp 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-202309.3' dh_auto_install cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/rdkit-202309.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EnumerateHeterocycles.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/AtomTypes.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/Fingerprinter.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState_VSA.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ShowMols.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/QED.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/SigFactory.py -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/__init__.py -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Supply.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/demo.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SDSupply.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Transform.py -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDData.sqlt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/RD.css -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg -- 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitAlignment.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Numerics/Alignment/AlignPoints.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics/rdAlignment.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitEigenSolvers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Numerics/EigenSolvers/PowerEigenSolver.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitOptimizer.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitOptimizer.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitOptimizer.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Numerics/Optimizer/BFGSOpt.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Numerics/Matrix.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Numerics/SquareMatrix.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Numerics/SymmMatrix.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Numerics/Vector.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Numerics/Conrec.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitForceField.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitForceField.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitForceField.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/Contrib.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/ForceField.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Params.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversion.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField/rdForceField.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeometry.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDistGeometry.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContrib.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry/DistGeom.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCatalogs.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCatalogs.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGraphMol.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGraphMol.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Atom.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Bond.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Canon.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/details.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Rings.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSmilesParse.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/primes.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDepictor.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDepictor.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDepictor.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdDepictor.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMarvinParser.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMarvinParser.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMarvinParser.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MarvinParser/MarvinParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFileParsers.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFileParsers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/CDXMLParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGenericGroups.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGenericGroups.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGenericGroups.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/GenericGroups/GenericGroups.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemReactions.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemReactions.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdChemReactions.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemTransforms.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2023.09.3 -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdfiltercatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFragCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitFragCatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdfragcatalog.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDescriptors.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDescriptors.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitO3AAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitO3AAlign.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolAlign.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdFMCS.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolHash.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolHash.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolHash.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolHash.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMMPA.so.1.2023.09.3 -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalClusterOptions.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalResult.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/CIPLabeler/CIPLabeler.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/CIPLabeler/TooManyNodesException.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDeprotect.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitDeprotect.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdDeprotect.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTrajectory.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitTrajectory.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 -- 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolInterchange.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKithc.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKithc.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKithc.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/cQuantize.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDPaths.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' mkdir -p /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3 mv /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3/dist-packages rm -f -rf /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12 ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202309.3/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-202309.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ rm -f -rf /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ dh_numpy3 dh_install mkdir -p /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit/ # cp /build/reproducible-path/rdkit-202309.3/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/reproducible-path/rdkit-202309.3/Docs/Book/_build/html /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit/ pg_buildext install /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit build-%v postgresql-%v-rdkit ### PostgreSQL 17 install ### make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/build-17' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/share/postgresql/17/extension' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/share/postgresql/17/extension' /usr/bin/install -c -m 755 rdkit.so '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so' /usr/bin/install -c -m 644 /build/reproducible-path/rdkit-202309.3/Code/PgSQL/rdkit/rdkit.control '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/share/postgresql/17/extension/' /usr/bin/install -c -m 644 rdkit--4.4.0.sql '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/share/postgresql/17/extension/' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode/rdkit' /bin/mkdir -p '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/ /usr/bin/install -c -m 644 rdkit_io.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 mol_op.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_op.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 sfp_op.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rxn_op.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rdkit_gist.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gist.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gin.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 low_gist.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 guc.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 cache.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 adapter.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bitstring.bc '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode'/rdkit/./ cd '/build/reproducible-path/rdkit-202309.3/debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/bitcode' && /usr/lib/llvm-19/bin/llvm-lto -thinlto -thinlto-action=thinlink -o rdkit.index.bc rdkit/rdkit_io.bc rdkit/mol_op.bc rdkit/bfp_op.bc rdkit/sfp_op.bc rdkit/rxn_op.bc rdkit/rdkit_gist.bc rdkit/bfp_gist.bc rdkit/bfp_gin.bc rdkit/low_gist.bc rdkit/guc.bc rdkit/cache.bc rdkit/adapter.bc rdkit/bitstring.bc make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/build-17' ### End 17 install ### ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202309.3/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' dh_installdocs -O--buildsystem=cmake debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_python3 -ppython3-rdkit I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming 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 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 DistGeom.so to DistGeom.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-x86_64-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' 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-202309.3' dh_missing --list-missing 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 debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example1.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example10.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example11.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example12.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example13.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example14.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example15.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example16.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example17.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example2.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example3.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example4.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example5.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example6.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example7.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example8.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example9.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Cartridge.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Cookbook.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedInC++.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedInPython.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Install.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Makefile exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Overview.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/RDKit_Book.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/api-docs.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/conf.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/AmideBond.rxn exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/bzr.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/bzr.smi exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/cdk2.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/chiral.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/input.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/invalid.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: 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 dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png 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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 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/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 The following debhelper tools have reported what they installed (with files per package) * dh_install: librdkit-dev (61), librdkit1t64 (118), 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-202309.3' 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: 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: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202309.3-7_amd64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-7_amd64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202309.3-7_all.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202309.3-7_all.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202309.3-7_amd64.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202309.3-7_amd64.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-7_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202309.3-7_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202309.3-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202309.3-7_amd64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202309.3-7_amd64.changes 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/3055525 and its subdirectories I: Current time: Mon Dec 8 07:39:18 -12 2025 I: pbuilder-time-stamp: 1765222758 Tue Nov 5 13:16:22 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Tue Nov 5 13:16:22 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Tue Nov 5 14:20:24 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Tue Nov 5 14:20:25 UTC 2024 I: rdkit_202309.3-7_amd64.changes: Format: 1.8 Date: Mon, 23 Sep 2024 07:04:09 -0400 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: 202309.3-7 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys 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 Changes: rdkit (202309.3-7) unstable; urgency=medium . * No-changes source-only upload. Checksums-Sha1: 8ea6383202c219610622fccedbd3263c58bd8748 415920 librdkit-dev_202309.3-7_amd64.deb 54f49f24704e884beda6b2fd44d695a415db762e 106232368 librdkit1t64-dbgsym_202309.3-7_amd64.deb 576379f3a573afb690ffaae1249645b6a5b46b2d 5040796 librdkit1t64_202309.3-7_amd64.deb 2f09c1e2bcb724589ecc33996ebb9d6121ca6597 1139136 postgresql-17-rdkit-dbgsym_202309.3-7_amd64.deb 269317983256ae601bbbcd17dc09db8b73c2e395 458400 postgresql-17-rdkit_202309.3-7_amd64.deb 745544f00e35aaab29ce40efb2bd14af3a638526 57564268 python3-rdkit-dbgsym_202309.3-7_amd64.deb 3e5add5e3d4f0d2cd4fbb10967d79f5fff7416d0 4609496 python3-rdkit_202309.3-7_amd64.deb 1a1021efde8b21ce451f648dc5d71911a52a2a83 13114084 rdkit-data_202309.3-7_all.deb 49db8ec2540da6ccae08e2ba3c1007872ad0196a 6101452 rdkit-doc_202309.3-7_all.deb b1983500b04436b03bde117e7ec52cb20481c9a8 18207 rdkit_202309.3-7_amd64.buildinfo Checksums-Sha256: 579a28e42a627f657b4779a9f72a3027c0ae9863ab2450ed6e360dd39ce2b80c 415920 librdkit-dev_202309.3-7_amd64.deb 7dfaca82a13c80656c2e2a8432a31b3bac29f848b64cf19e3998eec88c0bea6b 106232368 librdkit1t64-dbgsym_202309.3-7_amd64.deb 2cedc0934ce5591cdd90290f976864cf60160e5ad52937f33aa194767eb84067 5040796 librdkit1t64_202309.3-7_amd64.deb 0691622545f4de8a3523f4919945b63b22d4a988e618678b9ee9d16576d004dc 1139136 postgresql-17-rdkit-dbgsym_202309.3-7_amd64.deb 87436f969f8e61259c0390b82dcd676c3a0fa3ccedc4ecf322f2dd6b5fb104e7 458400 postgresql-17-rdkit_202309.3-7_amd64.deb baf563335001cc955bf822ddff3a3475de22fdd854e5199d68e48d67c4df98cf 57564268 python3-rdkit-dbgsym_202309.3-7_amd64.deb 33c367bf8a2437a6d5ca87644dab97bd52c388f12268558a9d0a4ff73edcbd2c 4609496 python3-rdkit_202309.3-7_amd64.deb d22dd7b9e39f7017406667bf4fc17a81240b3b4e37196f94232764196d0e7a2e 13114084 rdkit-data_202309.3-7_all.deb bacc5f02ec704e4d2be35d00d379f39df23f240ecc02e2e613ae2e336de4fe35 6101452 rdkit-doc_202309.3-7_all.deb 63ac047c6a8d56ce720f33ff1872c27526c63b97f15323f20beca676f095e621 18207 rdkit_202309.3-7_amd64.buildinfo Files: aa1ef476d7bff8ed028d1f71ab3e0df2 415920 libdevel optional librdkit-dev_202309.3-7_amd64.deb cdccfde3af03337b919d55807815b71b 106232368 debug optional librdkit1t64-dbgsym_202309.3-7_amd64.deb 2cd37b4ec15d15900b46f30066a2ee20 5040796 libs optional librdkit1t64_202309.3-7_amd64.deb 4dab8610fe4713f19b401739ea6ced70 1139136 debug optional postgresql-17-rdkit-dbgsym_202309.3-7_amd64.deb 09f1926768cb6f704ee20902b64d9ec5 458400 database optional postgresql-17-rdkit_202309.3-7_amd64.deb 265049475fcf50ae3c51f07776d393a3 57564268 debug optional python3-rdkit-dbgsym_202309.3-7_amd64.deb 703287b4a75a2476f28e12e5ba67c2af 4609496 python optional python3-rdkit_202309.3-7_amd64.deb dcd37816ab469b243d0a28e7334bfb6d 13114084 science optional rdkit-data_202309.3-7_all.deb e6c10a81acc6cd7ffe2f81a132592397 6101452 doc optional rdkit-doc_202309.3-7_all.deb aa3dea1017d297c312cd0513f3574f99 18207 science optional rdkit_202309.3-7_amd64.buildinfo Tue Nov 5 14:20:36 UTC 2024 I: diffoscope 282 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_26-23674.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/rdkit_202309.3-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/rdkit_202309.3-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/rdkit_202309.3-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/b1/rdkit_202309.3-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/b2/rdkit_202309.3-7_amd64.changes ## close_archive (total time: 0.002s) 0.001s 38 calls diffoscope.comparators.xz.XzContainer 0.000s 24 calls diffoscope.comparators.deb.DebContainer 0.000s 30 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 108.806s) 43.525s 1058 calls readelf 27.675s 134 calls diff 16.339s 38 calls xz 14.972s 2 calls objcopy 4.732s 220 calls objdump 0.607s 12 calls cmp 0.606s 12 calls cmp (external) 0.166s 22 calls strings 0.160s 33 calls js-beautify 0.024s 93 calls cmp (internal) ## compare_files (cumulative) (total time: 553.767s) 115.050s 1 call abc.DotChangesFile 114.277s 3 calls abc.DebFile 112.785s 6 calls abc.XzFile 104.222s 3 calls abc.DebDataTarFile 70.245s 2 calls abc.ElfFile 26.848s 10 calls diffoscope.comparators.elf.ElfCodeSection 6.640s 3 calls abc.JavaScriptFile 1.897s 37 calls diffoscope.comparators.elf.ElfSection 1.156s 3 calls abc.TarFile 0.451s 3 calls abc.Md5sumsFile 0.118s 3 calls diffoscope.comparators.elf.ElfStringSection 0.061s 1 call abc.TextFile 0.017s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 29.396s) 16.349s 38 calls diffoscope.comparators.xz.XzContainer 9.243s 9728 calls diffoscope.comparators.deb.DebTarContainer 3.699s 44 calls diffoscope.comparators.deb.DebContainer 0.105s 40 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 2.817s) 2.817s 50 calls linediff ## has_same_content_as (total time: 0.681s) 0.323s 9 calls abc.DebFile 0.266s 3 calls abc.DebDataTarFile 0.028s 37 calls diffoscope.comparators.elf.ElfSection 0.026s 63 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.024s 6 calls abc.Md5sumsFile 0.009s 3 calls abc.TarFile 0.002s 8 calls abc.TextFile 0.001s 3 calls abc.JavaScriptFile 0.001s 6 calls abc.XzFile 0.001s 2 calls abc.ElfFile 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: 123.661s) 123.648s 2 calls outputs 0.013s 1 call cleanup ## open_archive (total time: 0.005s) 0.004s 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: 3.548s) 3.542s 1 call html 0.004s 1 call text 0.002s 1 call json ## recognizes (total time: 20.074s) 10.034s 1880 calls diffoscope.comparators.utils.archive.ArchiveMember 5.072s 3524 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 4.075s 12 calls diffoscope.comparators.binary.FilesystemFile 0.893s 972 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 1.580s) 1.580s 155 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 2min 12.722s CPU time consumed: 1min 30.168s Tue Nov 5 14:22:56 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Tue Nov 5 14:22:56 UTC 2024 E: rdkit failed to build reproducibly in unstable on amd64. Tue Nov 5 14:22:59 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Nov 5 14:22:59 UTC 2024 I: Submitting 20K b1/rdkit_202309.3-7_amd64.buildinfo.asc Tue Nov 5 14:23:01 UTC 2024 I: Submitting 20K b2/rdkit_202309.3-7_amd64.buildinfo.asc Tue Nov 5 14:23:02 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Nov 5 14:23:02 UTC 2024 I: Done submitting .buildinfo files. Tue Nov 5 14:23:02 UTC 2024 I: Removing signed rdkit_202309.3-7_amd64.buildinfo.asc files: removed './b1/rdkit_202309.3-7_amd64.buildinfo.asc' removed './b2/rdkit_202309.3-7_amd64.buildinfo.asc'