I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 20 04:13:41 +14 2024 I: pbuilder-time-stamp: 1732025621 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/871424/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 19 14:13 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/871424/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/871424/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=af9cdda5e55f4cbcb3663e332a586700 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=871424 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fZ2ZwLUa/pbuilderrc_jdAd --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fZ2ZwLUa/b2 --logfile b2/build.log rdkit_202309.3-7.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/871424/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: arm64 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 ... 20084 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-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 395 MB of archives. After unpacking 2127 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 flex arm64 2.6.4-8.2+b3 [412 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-2 [337 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.0-1+b1 [248 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.3-1 [11.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.3-1 [14.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.3-1 [419 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 liblqr-1-0 arm64 0.4.2-2.1+b2 [27.0 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-8 [392 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libraw23t64 arm64 0.21.3-1+b1 [370 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 imagemagick-7-common all 8:7.1.1.39+dfsg1-2 [66.7 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libmagickcore-7.q16-10 arm64 8:7.1.1.39+dfsg1-2 [1648 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libmagickwand-7.q16-10 arm64 8:7.1.1.39+dfsg1-2 [267 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 postgresql-client-common all 266 [36.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 ssl-cert all 1.1.3 [16.8 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 postgresql-common all 266 [169 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 bison arm64 2:3.8.2+dfsg-1+b2 [1149 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libcatch2-dev arm64 3.7.1-0.4 [588 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 catch2 all 3.7.1-0.4 [5052 B] Get: 93 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.3-2 [23.3 MB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libclang-cpp19 arm64 1:19.1.3-2 [12.0 MB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libgc1 arm64 1:8.2.8-1 [241 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libobjc4 arm64 14.2.0-8 [39.5 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libobjc-14-dev arm64 14.2.0-8 [166 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libclang-common-19-dev arm64 1:19.1.3-2 [739 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 llvm-19-linker-tools arm64 1:19.1.3-2 [1098 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libclang1-19 arm64 1:19.1.3-2 [6844 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 clang-19 arm64 1:19.1.3-2 [112 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.0-1 [2265 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-2 [73.1 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.0-1 [9874 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 124 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 136 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2+b3 [4515 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 native-architecture all 0.2.3 [2108 B] Get: 149 http://deb.debian.org/debian unstable/main arm64 libgirepository-2.0-0 arm64 2.82.2-3 [130 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 girepository-tools arm64 2.82.2-3 [134 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-5+b1 [195 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 imagemagick-7.q16 arm64 8:7.1.1.39+dfsg1-2 [726 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 imagemagick arm64 8:7.1.1.39+dfsg1-2 [19.8 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b2 [13.0 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b2 [9128 B] Get: 158 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5 [153 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5 [47.9 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5 [60.3 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5 [106 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b1 [173 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b3 [55.6 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b2 [53.2 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5 [7358 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20241115-1 [22.7 MB] Get: 185 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 latexmk all 1:4.85-1 [501 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 188 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 uuid-dev arm64 2.40.2-11 [47.8 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 libblkid-dev arm64 2.40.2-11 [208 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83.0 arm64 1.83.0-3.2+b1 [234 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83-dev arm64 1.83.0-3.2+b1 [234 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-3.2+b1 [239 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83-dev arm64 1.83.0-3.2+b1 [245 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libboost-date-time1.83.0 arm64 1.83.0-3.2+b1 [230 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83.0 arm64 1.83.0-3.2+b1 [325 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83-dev arm64 1.83.0-3.2+b1 [374 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libboost-date-time1.83-dev arm64 1.83.0-3.2+b1 [239 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 201 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83.0 arm64 1.83.0-3.2+b1 [314 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-5+b1 [10.3 MB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83-dev arm64 1.83.0-3.2+b1 [335 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-3.2+b1 [261 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 206 http://deb.debian.org/debian unstable/main arm64 libboost-python1.83.0 arm64 1.83.0-3.2+b1 [309 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.7-3 [1982 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.7-3 [4792 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.12.7-1 [9980 B] Get: 212 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.12.7-1 [26.1 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libboost-python1.83-dev arm64 1.83.0-3.2+b1 [322 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libboost-python-dev arm64 1.83.0.2+b2 [3880 B] Get: 219 http://deb.debian.org/debian unstable/main arm64 libboost-regex-dev arm64 1.83.0.2+b2 [3852 B] Get: 220 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83.0 arm64 1.83.0-3.2+b1 [231 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83-dev arm64 1.83.0-3.2+b1 [232 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B] Get: 223 http://deb.debian.org/debian unstable/main arm64 libboost-thread1.83.0 arm64 1.83.0-3.2+b1 [266 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libboost-thread1.83-dev arm64 1.83.0-3.2+b1 [276 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libboost-thread-dev arm64 1.83.0.2+b2 [3616 B] Get: 226 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libcairo-script-interpreter2 arm64 1.18.2-2 [57.4 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libpng-dev arm64 1.6.44-2 [360 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 libfreetype-dev arm64 2.13.3+dfsg-1 [600 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 libfontconfig-dev arm64 2.15.0-1.1+b1 [411 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libffi-dev arm64 3.4.6-1 [57.0 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libsepol-dev arm64 3.7-1 [354 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 libpcre2-16-0 arm64 10.44-4 [230 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 libpcre2-32-0 arm64 10.44-4 [220 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 libpcre2-posix3 arm64 10.44-4 [60.4 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 libpcre2-dev arm64 10.44-4 [704 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libselinux1-dev arm64 3.7-3+b1 [164 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libmount-dev arm64 2.40.2-11 [28.9 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 libsysprof-capture-4-dev arm64 47.0-2 [48.9 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libgio-2.0-dev arm64 2.82.2-3 [1691 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libglib2.0-data all 2.82.2-3 [1275 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libglib2.0-bin arm64 2.82.2-3 [123 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libgio-2.0-dev-bin arm64 2.82.2-3 [162 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libglib2.0-dev-bin arm64 2.82.2-3 [51.5 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libglib2.0-dev arm64 2.82.2-3 [52.3 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libpixman-1-dev arm64 0.44.0-3 [11.4 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 x11proto-dev all 2024.1-1 [603 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 257 http://deb.debian.org/debian unstable/main arm64 libice-dev arm64 2:1.1.1-1 [73.0 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libsm-dev arm64 2:1.2.4-1 [38.0 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libxau-dev arm64 1:1.0.11-1 [23.9 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libxdmcp-dev arm64 1:1.1.2-3+b2 [40.6 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libxcb1-dev arm64 1.17.0-2+b1 [182 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libx11-dev arm64 2:1.8.10-2 [877 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libxcb-render0-dev arm64 1.17.0-2+b1 [119 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0-dev arm64 1.17.0-2+b1 [108 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libxext-dev arm64 2:1.3.4-1+b2 [105 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libxrender-dev arm64 1:0.9.10-1.1+b2 [35.7 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libcairo2-dev arm64 1.18.2-2 [43.0 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libcoordgen3 arm64 3.0.2-1+b2 [204 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 libcoordgen-dev arm64 3.0.2-1+b2 [46.9 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b1 [755 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1+b1 [131 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libinchi1.07 arm64 1.07.1+dfsg-5 [499 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libinchi-dev arm64 1.07.1+dfsg-5 [19.5 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.6-3+b2 [133 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libmaeparser1 arm64 1.3.1-1+b2 [84.6 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libmaeparser-dev arm64 1.3.1-1+b2 [13.6 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libncurses-dev arm64 6.5-2+b1 [338 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [210 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [51.8 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [33.5 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libpfm4 arm64 4.13.0+git83-g91970fe-1 [63.6 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libpq5 arm64 17.1-1 [216 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libpq-dev arm64 17.1-1 [144 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 librsvg2-2 arm64 2.59.1+dfsg-1 [1675 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 librsvg2-bin arm64 2.59.1+dfsg-1 [1799 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-1 [1058 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [751 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b2 [49.3 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libz3-dev arm64 4.13.3-1 [107 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 llvm-19-runtime arm64 1:19.1.3-2 [503 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 llvm-19 arm64 1:19.1.3-2 [14.7 MB] Get: 311 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.2-1+b1 [148 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 llvm-19-tools arm64 1:19.1.3-2 [486 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 llvm-19-dev arm64 1:19.1.3-2 [40.1 MB] Get: 315 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] Get: 317 http://deb.debian.org/debian unstable/main arm64 postgresql-client-17 arm64 17.1-1 [1957 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 postgresql-server-dev-17 arm64 17.1-1 [1306 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 postgresql-server-dev-all arm64 266 [20.8 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1 [350 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.16.0-1 [114 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 325 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 python3-commonmark all 0.9.1-6 [45.3 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 python3-greenlet arm64 3.1.0-1+b1 [178 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 335 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 python3-mdurl all 0.1.2-1 [9444 B] Get: 338 http://deb.debian.org/debian unstable/main arm64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 python3-mdit-py-plugins all 0.4.2-1 [32.4 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.4.7-4 [731 kB] Get: 341 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.4.7-4 [588 kB] Get: 345 http://deb.debian.org/debian unstable/main arm64 python3-myst-parser all 4.0.0-1 [78.7 kB] Get: 346 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 350 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.4.0-1+b1 [498 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 python3-sqlalchemy all 2.0.32+ds1-1 [1196 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 tex-gyre all 20180621-6 [6209 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2024.20241115-1 [4991 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 360 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] Fetched 395 MB in 4s (102 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 ... 20084 files and directories currently installed.) Preparing to unpack .../00-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../01-flex_2.6.4-8.2+b3_arm64.deb ... Unpacking flex (2.6.4-8.2+b3) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../02-libfftw3-double3_3.3.10-2_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.10-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../03-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../04-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../05-libpng16-16t64_1.6.44-2_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (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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Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Nov 19 14:15:31 UTC 2024. Universal Time is now: Tue Nov 19 14:15:31 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-3.2+b1) ... Setting up libsysprof-capture-4-dev:arm64 (47.0-2) ... Setting up libboost-serialization1.83.0:arm64 (1.83.0-3.2+b1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up libfontenc1:arm64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libpcre2-32-0:arm64 (10.44-4) ... Setting up libglib2.0-0t64:arm64 (2.82.2-3) ... No schema files found: doing nothing. 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Setting up libthai-data (0.1.29-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.0-1) ... Setting up librhash1:arm64 (1.4.5-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-system1.83-dev:arm64 (1.83.0-3.2+b1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libcoordgen3:arm64 (3.0.2-1+b2) ... Setting up libde265-0:arm64 (1.0.15-1+b2) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:arm64 (1.4.0-0.1+b1) ... Setting up libinchi1.07 (1.07.1+dfsg-5) ... Setting up libcatch2-dev (3.7.1-0.4) ... Setting up readline-common (8.2-5) ... Setting up libicu-dev:arm64 (72.1-5+b1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libbrotli-dev:arm64 (1.1.0-2+b6) ... Setting up libfmt10:arm64 (10.1.1+ds1-4) ... Setting up libsynctex2:arm64 (2024.20240313.70630+ds-5) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up libpotrace0:arm64 (1.16-2+b2) ... Setting up libmaeparser-dev:arm64 (1.3.1-1+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up postgresql-client-common (266) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libblkid-dev:arm64 (2.40.2-11) ... Setting up libllvm19:arm64 (1:19.1.3-2) ... Setting up catch2 (3.7.1-0.4) ... Setting up libz3-dev:arm64 (4.13.3-1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up flex (2.6.4-8.2+b3) ... Setting up libinchi-dev (1.07.1+dfsg-5) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.5-2+b1) ... Setting up gettext (0.22.5-2) ... Setting up libclang1-19 (1:19.1.3-2) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxau-dev:arm64 (1:1.0.11-1) ... Setting up libboost-chrono1.83-dev:arm64 (1.83.0-3.2+b1) ... Setting up libxpm4:arm64 (1:3.5.17-1+b2) ... Setting up libpcre2-dev:arm64 (10.44-4) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libice-dev:arm64 (2:1.1.1-1) ... Setting up libtool (2.4.7-8) ... Setting up libgirepository-2.0-0:arm64 (2.82.2-3) ... Setting up libselinux1-dev:arm64 (3.7-3+b1) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1+b1) ... 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Setting up texlive-binaries (2024.20240313.70630+ds-5) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20241115-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up librsvg2-bin (2.59.1+dfsg-1) ... Setting up python3 (3.12.7-1) ... Setting up libpython3.12-dev:arm64 (3.12.7-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b3) ... 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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: user script /srv/workspace/pbuilder/871424/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/871424/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/rdkit-202309.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202309.3-7_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202309.3-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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-aarch64-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/aarch64-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/aarch64-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/aarch64-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-3.31/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 CMake Warning (dev) at External/INCHI-API/CMakeLists.txt:102 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/aarch64-linux-gnu/libmaeparser.so' -- Found maeparser: /usr/include -- coordgen include dir set as /usr/include -- coordgen libraries set as '/usr/lib/aarch64-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/aarch64-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 (1.9s) -- Generating done (1.1s) 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-aarch64-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-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' /usr/bin/cmake 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh/hcdriver.c [ 1%] Built target inchi_support [ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh/hc.c [ 1%] Built target ringdecomposerlib_support [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 2%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file,CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2023.09.3 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 2%] Built target hc [ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 3%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 [ 3%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 /usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o /usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 3%] Built target rdkitCatch /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/ga.dir/link.d -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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2023.09.3 ../../lib/libRDKitga.so.1 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build make[4]: 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/base64.cpp [ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.cpp [ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd 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cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/MultiFPBReader.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2023.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 6%] Built target Catalogs [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/MaxMinPicker.cpp [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc && 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 6%] Built target testMatCalc [ 6%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/RDBoost.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2023.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh/Clustering.cpp [ 8%] Linking CXX executable dictTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 8%] Built target dictTestsCatch [ 9%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/SimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 9%] Built target SimDivPickers make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 9%] Built target testQuery [ 9%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 9%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.cpp [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.cpp [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.cpp [ 10%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o [ 10%] Building 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.cpp [ 11%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script 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Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp [ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 12%] Linking CXX executable pickersTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pickersTestsCatch.dir/link.d CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 12%] Built target pickersTestsCatch make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory 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make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 12%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/RDGeometryLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory 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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/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 [ 12%] Linking CXX executable testFPB cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testFPB.dir/link.d 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 13%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/testGrid.cpp [ 14%] Linking CXX executable testMultiFPB cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/Point.cpp [ 14%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 14%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 [ 14%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/InfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o 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directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 14%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 14%] Linking CXX executable testGrid cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 [ 14%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdSimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 14%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd 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-Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp [ 14%] Linking CXX executable testTransforms cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testTransforms.dir/link.d 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/ChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testChemicalFeatures.dir/link.d CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 15%] Built target testChemicalFeatures [ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 15%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 [ 16%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdAlignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 16%] Built target rdAlignment [ 16%] Built target cQuantize [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_FPB.cpp [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_BitOps.cpp [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_Utils.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /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])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ [ 17%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdInfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 17%] Built target rdInfoTheory [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp [ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/rdGeometry.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp:1348:36: warning: unused parameter 'mol' [-Wunused-parameter] 1348 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 18%] Built target rdGeometry [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/map:62, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h:14, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp:11: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp:96:57: required from here 96 | adata.d_isotopeInfoMap[isotope] = std::make_pair(mass, abundance); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp:72:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 72 | if (res < 0) { | ~~~~^~~ [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/BondIterators.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 19%] Linking CXX shared module ../../../rdkit/rdBase.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 19%] Built target rdBase [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.cpp [ 19%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.cpp /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 19%] Built target cDataStructs [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StereoGroup.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindStereo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/NontetrahedralStereo.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/WedgeBonds.cpp [ 21%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/GraphMol.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2023.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 21%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp [ 21%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 22%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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 [ 22%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/Trajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 22%] Built target Trajectory make -f 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Parser.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 22%] Built target MolCatalog make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.cpp make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make 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Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdqueries.cpp [ 22%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/Subgraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 23%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 23%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 23%] Built target GenericGroups make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 23%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 24%] Built target Optimizer make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdTrajectory.cpp [ 25%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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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 [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 28%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 [ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 28%] Built target rdtrajectory 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 28%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 28%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/ShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E 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"--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/testOptimizer.cpp [ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 28%] Built target SmilesParse make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp [ 28%] Linking CXX executable testOptimizer cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testOptimizer.dir/link.d CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 28%] Built target testOptimizer make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_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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-O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleBend.cpp [ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 [ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdMolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 29%] Built target rdMolTransforms make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 30%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/itertest.cpp [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 31%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 [ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 [ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-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 [ 33%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 34%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Nonbonded.cpp [ 34%] Linking CXX executable graphmolMemTest1 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/test2.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 library ../../../lib/libRDKitCIPLabeler.so 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/usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 34%] Built target CIPLabeler 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 36%] Built target subgraphsCatch [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.cpp [ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/OopBend.cpp [ 37%] Linking CXX executable testSubgraphs2 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testSubgraphs2.dir/link.d CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.cpp [ 37%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.cpp [ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/DistanceConstraint.cpp /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 27 | const MMFFStbn *mmffStbnParams) { | ^ [ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.cpp [ 39%] Linking CXX executable moliteratorTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.cpp [ 40%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 40%] Built target ForceField make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd 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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/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 [ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp [ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 40%] Built target MolAlign make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 40%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp [ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp [ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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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 [ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp [ 40%] Linking CXX executable graphmolqueryTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 40%] Built target graphmolqueryTest make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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 [ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 42%] Building CXX object 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp [ 42%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2023.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.cpp [ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp [ 43%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ 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Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp [ 43%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp [ 43%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.cpp [ 43%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp [ 43%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 43%] Linking CXX executable smaTest1 cd 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 43%] Built target smaTest1 make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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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library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/Abbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD 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CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp [ 43%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 43%] Built target MolChemicalFeatures make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu 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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 -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 43%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 43%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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../../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 43%] Built target FragCatalog make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 43%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 43%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 43%] Built 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp [ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp /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 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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 [ 43%] Linking CXX executable testReducedGraphs cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testReducedGraphs.dir/link.d CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp [ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time 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Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-aarch64-linux-gnu' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o 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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 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 45%] Built target rdMolChemicalFeatures [ 45%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 45%] Built target ForceFieldHelpers make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom 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Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 45%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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 [ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o [ 45%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-aarch64-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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-aarch64-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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 [ 45%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/RDInchiLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2023.09.3 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/aarch64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 [ 45%] Built target rdAbbreviations [ 45%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd 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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 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 45%] Built target rdFingerprintGenerator [ 45%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 /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 module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 45%] Built target rdDepictor [ 46%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 46%] Built target DistGeometry make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 46%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o [ 46%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 [ 46%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o [ 46%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 46%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdinchi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 46%] Built target rdinchi [ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o 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../../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 46%] 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileParser.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp [ 46%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 46%] Built target testDistGeom [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 46%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 46%] Built target O3AAlign [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp [ 47%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 47%] Built target DistGeom [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileWriter.cpp [ 47%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 47%] Built target rdForceField [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDWriter.cpp [ 48%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 48%] Built target DistGeomHelpers [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTWriter.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PDBParser.cpp [ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileWriter.cpp [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o cd 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/FileParsers.dir/MaeWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeWriter.cpp [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.cpp [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SequenceWriters.cpp.o -MF 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 [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd 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-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 [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/FileParsers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2023.09.3 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 50%] Built target FileParsers make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testChirality.cpp [ 51%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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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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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/resMolSupplierTest.cpp [ 53%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.d CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 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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 -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/WHIM.cpp [ 53%] Linking CXX executable hanoiTest cd 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testSGroup.cpp [ 53%] Linking CXX executable testMMFFForceField cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testMMFFForceField.dir/link.d CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Built target testMMFFForceField make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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[ 53%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_sgroups.cpp [ 53%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Linking CXX executable graphmoltestPickler cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 [ 53%] Built target graphmoltestChirality make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_adjustquery.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Built target graphmoltestPickler make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make 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Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o -MF CMakeFiles/smiTest1.dir/test.cpp.o.d -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/test.cpp [ 53%] Linking CXX executable graphmolOrganometallicsCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/graphmolOrganometallicsCatch.dir/link.d CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -o graphmolOrganometallicsCatch ../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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Built target graphmolOrganometallicsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/cxsmiles_test.cpp [ 54%] Linking CXX executable graphmolSGroupCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 [ 54%] Linking CXX executable pickleTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/graphmolSGroupCatch.dir/link.d CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a 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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 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/testDepictor.cpp [ 55%] Linking CXX executable graphmolAdjustQueryCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro 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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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 55%] Built target nontetrahedralCatch make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" [ 55%] Built target testSGroup make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMolSupplier.cpp [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testGeneralFileReader.cpp [ 55%] Linking CXX executable cxsmilesTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 55%] Built target cxsmilesTest make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp [ 56%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/Descriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 56%] Built target 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Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMolWriter.cpp [ 56%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testTpls.cpp [ 56%] Linking CXX executable testMultithreadedMolSupplier cd 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 56%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 57%] Linking CXX executable testGeneralFileReader cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testSequence.cpp [ 57%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testMol2ToMol.dir/link.d 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp [ 57%] Linking CXX executable graphmolTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 [ 57%] Linking CXX executable testSequence cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 [ 57%] Linking CXX executable testTplParser cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testSequence.dir/link.d CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so 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../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" [ 57%] Built target testTplParser 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/file_parsers_catch.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testPropertyLists.cpp [ 57%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp [ 57%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Built target graphmolMolOpsTest make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp [ 57%] Linking CXX executable smiTest1 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp [ 57%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 57%] Built target testExtendedStereoParsing 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 58%] Linking CXX executable depictorCatch cd 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../../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 58%] Built target depictorCatch 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp [ 58%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 [ 58%] Linking CXX executable chiralityTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 58%] Built target XYZFileParserCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 58%] Built target chiralityTestsCatch 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 /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)}) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ [ 59%] Linking CXX executable testMolSupplier cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp [ 59%] Linking CXX executable connectTheDotsTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/catch_tests.cpp [ 59%] Linking CXX executable testMolWriter cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 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Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 60%] Linking CXX executable smiTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/test1.cpp [ 60%] Linking CXX executable molfileStereoCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 60%] Built target molfileStereoCatchTest 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 60%] Linking CXX executable cdxmlParserCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory 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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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 60%] Built target testPropertyLists make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 60%] Linking CXX executable testGenericGroups cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script 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../../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 60%] Built target testGenericGroups make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make 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Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testATF.cpp [ 61%] Linking CXX executable testFragCatalog cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 61%] Built target testFragCatalog make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testEEM.cpp [ 61%] Linking CXX executable substructTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 61%] Linking CXX executable testWHIM cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 [ 61%] Linking CXX executable testCoulombMat cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 [ 61%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp /usr/bin/c++ -g -O2 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../../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 61%] Built target testWHIM make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make 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../../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 61%] Built target testCoulombMat make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make 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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 -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 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:437:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 437 | python::list atomprops) { | ^ [ 61%] Linking CXX executable test3D cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /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/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp [ 62%] Linking CXX executable fileParsersCatchTest cd 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 62%] Built target fileParsersCatchTest make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 62%] Linking CXX executable testMHFPFingerprint cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 63%] Built target descriptorsTestCatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp [ 64%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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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 [ 64%] Linking CXX executable testMolTransforms cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 64%] Built target testMolTransforms make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" [ 65%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp [ 65%] Linking CXX executable testCrystalForceField cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Built target testCrystalForceField make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testMolAlign.cpp [ 65%] Linking CXX executable fpGenTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp [ 65%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 [ 65%] Linking CXX executable testMMFFForceFieldHelpers cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdfragcatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so 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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 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Built target rdfragcatalog make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp [ 65%] Linking CXX executable fpTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fpTestCatch.dir/link.d CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Built target fpTestCatch make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 65%] Linking CXX executable testUFFForceFieldHelpers cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testUFFForceFieldHelpers.dir/link.d CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:17, from /build/reproducible-path/rdkit-202309.3/Code/Numerics/Matrix.h:14, from /build/reproducible-path/rdkit-202309.3/Code/Numerics/SquareMatrix.h:14, from /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.h:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h:14, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here 643 | oscores.push_back(std::make_pair(rmsd, score)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 65%] Linking CXX executable testMolAlign cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Built target testMolAlign 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/test1.cpp [ 65%] Linking CXX executable testFingerprintGenerators cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 66%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 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/usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 66%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 [ 66%] Built target rdDistGeom make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 66%] Linking CXX executable distGeomHelpersCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 /usr/bin/c++ 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.cpp [ 66%] Linking CXX executable molAlignCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 [ 66%] Linking CXX executable testShapeHelpers cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake 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Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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../../../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/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/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 66%] Linking CXX executable testO3AAlign cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 [ 66%] Linking CXX executable 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../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT External/INCHI-API/CMakeFiles/testInchi.dir/test.cpp.o -MF CMakeFiles/testInchi.dir/test.cpp.o.d -o CMakeFiles/testInchi.dir/test.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/INCHI-API/test.cpp [ 68%] Linking CXX executable testDistGeomHelpers cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.cpp [ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../../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 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/MDLParser.cpp [ 69%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/trajectoryTest.dir/link.d CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-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 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CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 69%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Seed.cpp [ 69%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 69%] Built target MMPA make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 69%] Linking CXX executable molInterchangeTest1 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/molInterchangeTest1.dir/link.d CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 69%] Linking CXX executable molInterchangeCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 [ 69%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/molInterchangeCatchTest.dir/link.d CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2023.09.3 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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 69%] Built target MolHash make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build make[4]: Entering directory 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp [ 69%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp [ 69%] Linking CXX executable testInchi cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp [ 72%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 72%] Built target rdMMPA [ 72%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionUtils.cpp [ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 72%] Built target rdMolHash [ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp [ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ 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CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp [ 72%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp [ 73%] Linking CXX executable molHashCatchTest cd 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../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 73%] Built target molHashCatchTest [ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 75%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 75%] Linking CXX executable testCIPLabeler cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testCIPLabeler.dir/link.d CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o 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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/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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 75%] Built target testCIPLabeler /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 [ 75%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp [ 76%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testReaction.cpp [ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o [ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" [ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o [ 76%] Linking CXX executable testRascalCluster cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 78%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 78%] Built target rdRascalMCES make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 78%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:17, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:19, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:16: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:771:42: required from here 771 | auto new_mins = getAtomCoords(make_pair(x_min, y_min)); | ~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 79%] Linking CXX executable testRascalMCES cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testRascalMCES.dir/link.d CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 79%] Built target testRascalMCES make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build [ 79%] Linking CXX executable testFMCS cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdmolops.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testFMCS.dir/link.d CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 79%] Built target testFMCS [ 79%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 79%] Linking CXX executable testReactionFingerprints cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 79%] Built target testReactionFingerprints [ 79%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 79%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 79%] Linking CXX executable testEnumeration cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration 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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 [ 79%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/Deprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2023.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o 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object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 79%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 79%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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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 [ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 81%] Linking CXX executable rxnTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 81%] Built target rxnTestCatch [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.cpp [ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp [ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = long int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ [ 83%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 83%] 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 83%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -MF CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o.d -o CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/testMrvToMol.cpp [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp In file included from /usr/include/c++/14/algorithm:60: 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/aarch64-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/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp [ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp [ 83%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.h:19, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.cpp:13: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.cpp:165:47: required from here 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.y)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp [ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp [ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolDraw2DJS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextJS.cpp [ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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../../../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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Atom.cpp [ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp [ 85%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../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 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so 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../../../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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libcairo.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 85%] Built target MolDraw2D make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend make[4]: Entering directory 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Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 85%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdmolops.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/TautomerQuery.cpp [ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Bond.cpp [ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeWriter.cpp [ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDMolSupplier.cpp In file included from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, 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 file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, 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:48:28: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /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:48:28: note: '' declared here 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, 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:48:28: /usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ /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:48:28: note: '' declared here 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Mol.cpp [ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdMolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../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/aarch64-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/aarch64-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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 87%] Built target rdMolEnumerator 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 87%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 87%] Built target TautomerQuery 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:21, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:1592:46: required from here 1592 | drawer.getAtomCoords(std::make_pair(ocoords.x, ocoords.y)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp [ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp [ 88%] Linking CXX executable testMolEnumerator cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 /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 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 88%] Built target testMolEnumerator make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp [ 88%] Linking CXX executable testReaction cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 [ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testReaction.dir/link.d CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 88%] Built target testReaction make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 89%] Linking CXX executable moldraw2DRxnTest1 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.cpp [ 92%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testCharge.cpp /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdmolfiles.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testTautomer.cpp [ 93%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/GeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 93%] Built target GeneralizedSubstruct make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/test2.cpp make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testFragment.cpp [ 93%] Linking CXX executable molNormalizeTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/catch_tests.cpp [ 93%] Linking CXX executable molValidateTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp [ 93%] Linking CXX executable molStandardizeSmallTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 93%] Built target molStandardizeSmallTest make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp [ 94%] Linking CXX executable molChargeTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 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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/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' 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-aarch64-linux-gnu' [ 94%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 94%] Linking CXX executable molStandardizeTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 94%] Built target molStandardizeTest 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 95%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script 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/build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 95%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdchem.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../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/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/aarch64-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 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 95%] Built target rdchem make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu 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CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp [ 95%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 [ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp /usr/bin/c++ -g -O2 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/usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 96%] Built target moldraw2DTestCatch [ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 96%] Built target ScaffoldNetwork make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory 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Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp [ 97%] Linking CXX executable molTautomerTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/molTautomerTest.dir/link.d CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 97%] Built target molTautomerTest make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 97%] Linking CXX executable tautomerQueryTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a 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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/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 98%] Built target tautomerQueryTestCatch [ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ 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-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 [ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 [ 98%] Linking CXX executable generalizedSubstructCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.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 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-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 [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script 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CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp [ 99%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 99%] Built target RGroupDecomposition make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f 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CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/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 -DrdRGroupDecomposition_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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 99%] Linking CXX executable testScaffoldNetwork cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testScaffoldNetwork.dir/link.d CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 /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 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../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 99%] Built target rdScaffoldNetwork /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file,CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now 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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/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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' [ 99%] Built target SubstructLibrary make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target testRGroupDecompInternals [100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdMolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../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/aarch64-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/aarch64-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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target rdMolStandardize [100%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target substructLibraryTest [100%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 [100%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 /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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target rgroupCatchTests /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../../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/aarch64-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/aarch64-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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target rdRGroupDecomposition [100%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 /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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target substructLibraryCatchTest [100%] Linking CXX executable testRGroupDecomp cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target testRGroupDecomp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file,CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../../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/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target rdSubstructLibrary make[3]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' STATIC_LINK=0 RDKIT_LIBDIR=/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -moutline-atomics -g -g -O2 -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -L/build/reproducible-path/rdkit-202309.3/obj-aarch64-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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files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/RDGeneral Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/hash Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/hash/detail Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.h... 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... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... 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... 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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... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.h... 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... 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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... 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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... 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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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[ 98%] source/rdkit.utils reading sources... [ 99%] source/rdkit.utils.cactvs reading sources... [ 99%] source/rdkit.utils.chemutils reading sources... [ 99%] source/rdkit.utils.fileutils reading sources... [100%] source/rdkit.utils.listutils reading sources... [100%] source/rdkit.utils.spiral /build/reproducible-path/rdkit-202309.3/Docs/Book/BackwardsIncompatibleChanges.md:49: WARNING: duplicate label changes to canonicalization, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/BackwardsIncompatibleChanges.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Cartridge.md:732: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202309.3/Docs/Book/BackwardsIncompatibleChanges.md /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:1733: WARNING: Title underline too short. Contiguous Rotatable Bonds ========================= /build/reproducible-path/rdkit-202309.3/Docs/Book/Cookbook.rst:1733: WARNING: Title underline too short. 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... [ 5%] C++Examples/example1.cpp copying downloadable files... [ 11%] C++Examples/example2.cpp copying downloadable files... [ 16%] C++Examples/example3.cpp copying downloadable files... [ 21%] C++Examples/example4.cpp copying downloadable files... [ 26%] C++Examples/example5.cpp copying downloadable files... [ 32%] C++Examples/example6.cpp copying downloadable files... [ 37%] C++Examples/example7.cpp copying downloadable files... [ 42%] C++Examples/example8.cpp copying downloadable files... [ 47%] C++Examples/example9.cpp copying downloadable files... [ 53%] ../Code/GraphMol/Bond.h copying downloadable files... [ 58%] C++Examples/example10.cpp copying downloadable files... [ 63%] C++Examples/CMakeLists.txt copying downloadable files... [ 68%] C++Examples/example11.cpp copying downloadable files... [ 74%] C++Examples/example12.cpp copying downloadable files... [ 79%] C++Examples/example13.cpp copying downloadable files... [ 84%] C++Examples/example17.cpp copying downloadable files... [ 89%] C++Examples/example14.cpp copying downloadable files... [ 95%] C++Examples/example15.cpp copying downloadable files... [100%] C++Examples/example16.cpp copying static files... done copying extra files... done copying assets: done writing output... [ 0%] BackwardsIncompatibleChanges writing output... [ 1%] Cartridge writing output... [ 1%] Cookbook writing output... [ 1%] GettingStartedInC++ writing output... [ 2%] GettingStartedInPython writing output... [ 2%] Install writing output... [ 2%] Overview writing output... [ 3%] RDKit_Book writing output... [ 3%] api-docs writing output... [ 3%] data/README writing output... [ 4%] index writing output... [ 4%] source/rdkit writing output... [ 4%] source/rdkit.Avalon writing output... [ 5%] source/rdkit.Avalon.pyAvalonTools writing output... [ 5%] source/rdkit.Chem writing output... [ 5%] source/rdkit.Chem.AllChem writing output... [ 6%] source/rdkit.Chem.AtomPairs writing output... 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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-aarch64-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202309.3 PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu//lib:" PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/:/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu//lib:" dh_auto_test cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j12 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/External/INCHI-API/testInchi 1: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/External/CoordGen/testCoordGen 2: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-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-aarch64-linux-gnu/Code/RDGeneral/testDict 4: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/RDGeneral/testRDValue 5: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/RDGeneral/testConcurrentQueue 6: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/RDGeneral/dictTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/RDGeneral/logTestsCatch 8: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/DataStructs/testDataStructs 9: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/DataStructs/testFPB 10: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/DataStructs/testMultiFPB 11: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 1: [04:48:23] ------------------------------------- 1: [04:48:23] ------------------------------------- 1: [04:48:23] ------------------------------------- 1: [04:48:23] ------------------------------------- 1: [04:48:23] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored 1: [04:48:23] ------------------------------------- 1: [04:48:23] ------------------------------------- 1: [04:48:23] ------------------------------------- 1: [04:48:23] Test multithreading 1: reading molecules 1: generating reference data 1: processing 1: launch :0 1: launch :1 1: launch :2 1: launch :3 1: [04:48:23] 1: 1: **** 1: Test Assert 1: Expression Failed: 1: Violation occurred on line 51 in file ./External/INCHI-API/test.cpp 1: Failed Expression: inchi == inchi2 1: **** 1: 1: [04:48:23] Invalid InChI prefix in generating InChI Key 1: [04:48:23] 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: 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: 0.3628 0.5403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5014 1.0435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.3692 0.5467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -2.2334 1.0497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -3.1012 0.5529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -1.3728 -0.4533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: -0.5086 -0.9565 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2: 0.3594 -0.4597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 1.2234 -0.9627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.0912 -0.4657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.0948 0.5341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2: 2.9554 -0.9689 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: [04:48:23] Testing Github940: property dictionaries leaking memory 4: [04:48:23] done 4: Testing RDValue 4: Testing RDAny 4: dict set int vect 4: dict get int vect 4: static boost any:0.04702 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: [04:48:23] 6: ----------------------------------------- 6: [04:48:23] Finished: testPushAndPop() 6: [04:48:23] 6: ----------------------------------------- 6: [04:48:23] 6: ----------------------------------------- 7: Randomness seeded to: 3067645734 7: =============================================================================== 7: All tests passed (32 assertions in 2 test cases) 7: 8: [04:48:23] should not be silent 8: [04:48:23] should not be silent 8: Randomness seeded to: 2825955281 8: [04:48:23] should not be silent 8: [04:48:23] should not be silent 8: [04:48:23] should not be silent 8: [04:48:23] should not be silent 8: [04:48:23] should not be silent 8: [04:48:23] should not be silent 8: [04:48:23] should not be silent 8: [04:48:23] 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 1/223 Test #5: testRDValue ............................ Passed 0.16 sec 2/223 Test #7: dictTestsCatch ......................... Passed 0.12 sec 3/223 Test #8: logTestsCatch .......................... Passed 0.10 sec 4/223 Test #9: testDataStructs ........................ Passed 0.09 sec 5/223 Test #10: testFPB ................................ Passed 0.07 sec 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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/Code/Geometry/testTransforms 16: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/Geometry/testGrid 17: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry 17: Test timeout computed to be: 1500 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: 16: **************************************** 16: testPointND 16: **************************************** 16: testPointOps3D 16: **************************************** 16: testPointOps2D 16: **************************************** 16: test12D 16: ref1: 2.99108 4.23979 ref2: 2.40124 2.03435 16: pt1: 0.590744 2.7266 pt2: 0.987342 2.27228 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: **************************************** 6/223 Test #2: testCoordGen ........................... Passed 0.29 sec 7/223 Test #11: testMultiFPB ........................... Passed 0.13 sec 8/223 Test #16: testTransforms ......................... Passed 0.02 sec test 18 Start 18: geometryTestsCatch 18: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch 18: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-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-aarch64-linux-gnu/Code/Numerics/testMatrices 20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics 20: Test timeout computed to be: 1500 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: 2087473925 18: =============================================================================== 18: All tests passed (50 assertions in 5 test cases) 18: 20: [04:48:23] ----------------------------------------- 20: [04:48:23] Testing RDNumerics: vectors and matrices Code 20: [04:48:23] --------------------------------------- 20: [04:48:23] test1Vector 20: [04:48:23] --------------------------------------- 20: [04:48:23] test2Matrix 20: [04:48:23] --------------------------------------- 20: [04:48:23] test3SquareMatrix 20: [04:48:23] --------------------------------------- 20: [04:48:23] test4SymmMatrix 9/223 Test #17: testGrid ............................... Passed 0.08 sec 10/223 Test #18: geometryTestsCatch ..................... Passed 0.06 sec 11/223 Test #20: testMatrices ........................... Passed 0.02 sec test 21 Start 21: testConrec 21: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/testConrec 21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment 22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap 23: Test timeout computed to be: 1500 1: [04:48:23] Invalid InChI prefix in generating InChI Key 1: [04:48:23] 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: terminate called after throwing an instance of 'Invar::Invariant' 1: what(): Expression Failed: 21: Randomness seeded to: 1475704069 21: 21: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 21: testConrec is a Catch2 v3.7.1 host application. 21: Run with -? for options 21: 21: ------------------------------------------------------------------------------- 21: connectLineSegments 21: basics 21: ------------------------------------------------------------------------------- 21: ./Code/Numerics/testConrec.cpp:90 21: ............................................................................... 21: 21: ./Code/Numerics/testConrec.cpp:130: FAILED: 21: CHECK( contours.size() == 74 ) 21: with expansion: 21: 177 == 74 21: 21: =============================================================================== 21: test cases: 3 | 2 passed | 1 failed 21: assertions: 179 | 178 passed | 1 failed 21: 22: ----------------------------------------- 22: Testing Alignment Code 22: --------------------------------------- 22: testBasic 22: --------------------------------------- 22: testTriangle 22: --------------------------------------- 22: testFourPts 22: --------------------------------------- 22: testReflection 22: --------------------------------------- 12/223 Test #1: testInchi ..............................Subprocess aborted***Exception: 0.44 sec [04:48:23] ------------------------------------- [04:48:23] ------------------------------------- [04:48:23] ------------------------------------- [04:48:23] ------------------------------------- [04:48:23] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored [04:48:23] ------------------------------------- [04:48:23] ------------------------------------- [04:48:23] ------------------------------------- [04:48:23] Test multithreading reading molecules generating reference data processing launch :0 launch :1 launch :2 launch :3 [04:48:23] **** Test Assert Expression Failed: Violation occurred on line 51 in file ./External/INCHI-API/test.cpp Failed Expression: inchi == inchi2 **** [04:48:23] Invalid InChI prefix in generating InChI Key [04:48:23] **** Test Assert Expression Failed: Violation occurred on line 45 in file ./External/INCHI-API/test.cpp Failed Expression: key2 == keys[i] **** [04:48:23] Invalid InChI prefix in generating InChI Key [04:48:23] **** Test Assert Expression Failed: Violation occurred on line 45 in file ./External/INCHI-API/test.cpp Failed Expression: key2 == keys[i] **** terminate called after throwing an instance of 'Invar::Invariant' what(): Expression Failed: 13/223 Test #21: testConrec .............................***Failed 0.06 sec Randomness seeded to: 1475704069 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ testConrec is a Catch2 v3.7.1 host application. Run with -? for options ------------------------------------------------------------------------------- connectLineSegments basics ------------------------------------------------------------------------------- ./Code/Numerics/testConrec.cpp:90 ............................................................................... ./Code/Numerics/testConrec.cpp:130: FAILED: CHECK( contours.size() == 74 ) with expansion: 177 == 74 =============================================================================== test cases: 3 | 2 passed | 1 failed assertions: 179 | 178 passed | 1 failed 14/223 Test #22: testAlignment .......................... Passed 0.04 sec test 24 Start 24: testOptimizer 24: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer 24: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField 25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField 26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF 26: Test timeout computed to be: 1500 24: ------------------------------------- 24: Testing linear search. 24: done 24: ------------------------------------- 24: Testing BFGS optimization. 24: done 15/223 Test #24: testOptimizer .......................... Passed 0.04 sec 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-aarch64-linux-gnu/Code/ForceField/Wrap 27: Test timeout computed to be: 1500 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. 26: ------------------------------------- 26: Official MMFF validation suite. 14: ......... 14: ---------------------------------------------------------------------- 14: Ran 9 tests in 0.013s 14: 14: OK 13: ...... 13: ---------------------------------------------------------------------- 13: Ran 6 tests in 0.002s 13: 13: OK 25: done 25: ------------------------------------- 25: Unit tests for copying UFF ForceFields. 25: done 25: ------------------------------------- 25: Unit test for UFF butane scan. 3: .... 3: ---------------------------------------------------------------------- 3: Ran 4 tests in 0.041s 3: 3: OK 26: 26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 16/223 Test #13: pyDiscreteValueVect .................... Passed 0.44 sec test 28 Start 28: testDistGeom 28: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom 28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom 28: Test timeout computed to be: 1500 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: 17/223 Test #14: pySparseIntVect ........................ Passed 0.45 sec test 29 Start 29: pyDistGeom 29: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" 29: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap 29: Test timeout computed to be: 1500 15: ......... 15: ---------------------------------------------------------------------- 15: Ran 9 tests in 0.081s 15: 15: OK 19: ........... 19: ---------------------------------------------------------------------- 19: Ran 11 tests in 0.012s 19: 19: OK 19: Testing Geometry wrapper 18/223 Test #28: testDistGeom ........................... Passed 0.05 sec test 30 Start 30: graphmolTest1 30: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 30: Test timeout computed to be: 1500 4: dynamic boost any:0.237781 s 30: Atoms: 30: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 30: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 30: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 30: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 30: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 30: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 30: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 30: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 30: 8 22 Ti chg: 0 deg: 1 exp: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: getExplicitValence() called without call to calcExplicitValence() 30: Violation occurred on line 298 in file ./Code/GraphMol/Atom.cpp 30: Failed Expression: d_explicitValence > -1 30: **** 30: 30: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 30: Bonds: 30: 0 0->1 order: 1 conj?: 0 aromatic?: 0 30: 1 1->2 order: 2 conj?: 0 aromatic?: 0 30: 2 2->3 order: 1 conj?: 0 aromatic?: 0 30: 3 0->4 order: 1 conj?: 0 aromatic?: 0 30: 4 5->6 order: 3 conj?: 0 aromatic?: 0 30: 5 6->7 order: 1 conj?: 0 aromatic?: 0 30: 6 7->8 order: 2 conj?: 0 aromatic?: 0 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: bond already exists 30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp 30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 30: **** 30: 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: bond already exists 30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp 30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 30: **** 30: 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: attempt to add self-bond 30: Violation occurred on line 379 in file ./Code/GraphMol/RWMol.cpp 30: Failed Expression: atomIdx1 != atomIdx2 30: **** 30: 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: bond already exists 30: Violation occurred on line 441 in file ./Code/GraphMol/ROMol.cpp 30: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 30: **** 30: 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: attempt to add self-bond 30: Violation occurred on line 439 in file ./Code/GraphMol/ROMol.cpp 30: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 30: **** 30: 30: [04:48:23] Explicit valence for atom # 0 B, 4, is greater than permitted 30: [04:48:23] Explicit valence for atom # 0 B, 5, is greater than permitted 30: [04:48:23] 30: 30: **** 30: Post-condition Violation 30: Element 'Xx' not found 30: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 30: Failed Expression: anum > -1 30: **** 30: 30: [04:48:23] ------------------------------------- 30: [04:48:23] Test github381: thread-safe initialization of the periodic table 19/223 Test #3: pyCoordGen ............................. Passed 0.74 sec test 31 Start 31: graphmolcpTest 31: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest 31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 31: Test timeout computed to be: 1500 31: 31: 31: 31: COPY 20/223 Test #19: testPyGeometry ......................... Passed 0.46 sec test 32 Start 32: graphmolqueryTest 32: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest 32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 32: Test timeout computed to be: 1500 21/223 Test #31: graphmolcpTest ......................... Passed 0.04 sec test 33 Start 33: graphmolMolOpsTest 33: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest 33: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 23: ..... 23: ---------------------------------------------------------------------- 23: Ran 5 tests in 0.009s 23: 23: OK 23: Testing Alignment Wrapper code: 30: [04:48:23] done 30: [04:48:23] ------------------------------------- 30: [04:48:23] Test github1041: Segfault for atom with no owner (expect some warnings) 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: no owner 30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 30: Failed Expression: dp_mol 30: **** 30: 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: no owner 30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h 30: Failed Expression: dp_mol 30: **** 30: 30: [04:48:23] done 30: [04:48:23] ------------------------------------- 30: [04:48:23] Test github1041: Segfault for atom with no owner (expect some warnings) 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: no owner 30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 30: Failed Expression: dp_mol 30: **** 30: 30: [04:48:23] 30: 30: **** 30: Pre-condition Violation 30: no owner 30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h 30: Failed Expression: dp_mol 30: **** 30: 30: [04:48:23] done 30: [04:48:23] ------------------------------------- 30: [04:48:23] Test github1453: RWMol.clear() should reset the numBonds count. 30: [04:48:23] done 30: [04:48:23] ------------------------------------- 30: [04:48:23] Test range-based for loops. 30: [04:48:23] done 30: [04:48:23] ------------------------------------- 30: [04:48:23] Test github1642: Atom index type is too low for big molecules. 32: [04:48:23] ---------------------- Test1 22/223 Test #15: pyFPB .................................. Passed 0.57 sec test 34 Start 34: graphmoltestChirality 34: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality 34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test2 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test3 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test4 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test5 32: [04:48:23] Done! 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test issue 2892580 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test github issue 53: query molecules not matching [R] 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test queries using qualifiers instead of == 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test Github issue 165: radicals not used in atom-atom matching 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test extra atom queries 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test extra bond queries 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test num heteroatom neighbor queries 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test atom type queries 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Test Github #2471: dummy atom queries are flagged as complex 32: [04:48:23] Done! 32: [04:48:23] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() 32: [04:48:23] Done! 4: static RDAny:0.027508 s 23/223 Test #32: graphmolqueryTest ...................... Passed 0.06 sec test 35 Start 35: graphmoltestPickler 35: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler 35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 33: 1 1 2 33: 1 1 1 33: 2 1 0.75 33: path: 2 33: [04:48:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 33: [04:48:23] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored 33: [04:48:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 33: [04:48:23] Explicit valence for atom # 0 B, 5, is greater than permitted 33: [04:48:23] Explicit valence for atom # 1 C, 5, is greater than permitted 33: [04:48:23] Explicit valence for atom # 1 C, 5, is greater than permitted 33: [04:48:23] Explicit valence for atom # 1 C, 5, is greater than permitted 33: [04:48:23] Explicit valence for atom # 1 Si, 7, is greater than permitted 25: done 24/223 Test #25: testUFFForceField ...................... Passed 0.44 sec test 36 Start 36: graphmoltestPicklerGlobalSetting 36: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 34: -------------------------- 34: -------------------------- 34: C/C=C/C(C)Cl 34: [04:48:23] Conflicting single bond directions around double bond at index 2. 34: [04:48:23] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [04:48:23] Conflicting single bond directions around double bond at index 4. 34: [04:48:23] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [04:48:23] Conflicting single bond directions around double bond at index 15. 34: [04:48:23] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [04:48:23] Conflicting single bond directions around double bond at index 2. 34: [04:48:23] BondStereo set to STEREONONE and single bond directions set to NONE. 34: [04:48:23] Conflicting single bond directions around double bond at index 1. 34: [04:48:23] BondStereo set to STEREONONE and single bond directions set to NONE. 35: [04:48:23] ------------------------------------- 35: [04:48:23] Testing String Pickle Roundtrips. 34: -------------------------------------------------- 25/223 Test #34: graphmoltestChirality .................. Passed 0.09 sec test 37 Start 37: graphmolIterTest 37: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest 37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 36: [04:48:23] done 26/223 Test #23: pyAlignment ............................ Passed 0.53 sec 27/223 Test #36: graphmoltestPicklerGlobalSetting ....... Passed 0.05 sec test 38 Start 38: hanoiTest 38: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest 38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 33: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 28/223 Test #37: graphmolIterTest ....................... Passed 0.05 sec test 40 Start 40: resMolSupplierTest 40: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest 40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 33: [04:48:24] non-ring atom 0 marked aromatic 33: [04:48:24] non-ring atom 0 marked aromatic 33: [04:48:24] Conflicting single bond directions around double bond at index 17. 33: [04:48:24] BondStereo set to STEREONONE and single bond directions set to NONE. 33: starting ring finding 33: done 33: starting ring finding 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing reading existing pickle file (v2). 29/223 Test #39: graphmolMemTest1 ....................... Passed 0.04 sec test 41 Start 41: molBundleTest 41: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest 41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 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 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 33: [04:48:24] WARNING: not removing hydrogen atom with dummy atom neighbors 33: ------------------------------- 33: [04:48:24] Explicit valence for atom # 0 N, 4, is greater than permitted 30/223 Test #41: molBundleTest .......................... Passed 0.05 sec test 42 Start 42: testSGroup 42: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup 42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 33: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 33: [04:48:24] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 33: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 33: [04:48:24] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 33: [04:48:24] WARNING: not removing hydrogen atom with dummy atom neighbors 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing combining molecules using pickles. 35: Atoms: 35: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 35: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 35: Bonds: 35: 0 0->1 order: 1 conj?: 0 aromatic?: 0 35: 1 1->2 order: 1 conj?: 0 aromatic?: 0 35: 2 2->0 order: 1 conj?: 0 aromatic?: 0 35: 3 3->4 order: 1 conj?: 0 aromatic?: 0 35: 4 4->5 order: 1 conj?: 0 aromatic?: 0 35: 5 5->6 order: 1 conj?: 0 aromatic?: 0 35: 6 6->3 order: 1 conj?: 0 aromatic?: 0 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing Issue164: Roundtrip Pickle Failure. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing Issue219: Pickle Failure with Conformations. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing Issue220: Pickle problems with bond stereochemistry. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing query serialization. 35: [04:48:24] C=[$(C=O)] 35: [04:48:24] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing radical handling in pickles. 35: [04:48:24] done 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing sf.net issue 2788233. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing sf.net issue 3202580. 35: mass! 13.0034 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing sf.net issue 3316407. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] 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 31/223 Test #42: testSGroup ............................. Passed 0.05 sec test 43 Start 43: test-valgrind 43: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind 43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 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 32/223 Test #43: test-valgrind .......................... Passed 0.04 sec test 44 Start 44: graphmolTestsCatch 44: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 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 29: ...... 29: ---------------------------------------------------------------------- 29: Ran 6 tests in 0.001s 29: 29: OK 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 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: * * 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 27: ...[04:48:24] Molecule does not have explicit Hs. Consider calling AddHs() 27: [04:48:24] 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: 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(*)* 44: Randomness seeded to: 351457576 44: [04:48:24] WARNING: not removing hydrogen atom without neighbors 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [04:48:24] Explicit valence for atom # 1 N, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 1 N, 6, is greater than permitted 44: [04:48:24] Explicit valence for atom # 1 N, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 1 N, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 2 O, 3, is greater than permitted 44: [04:48:24] Explicit valence for atom # 2 O, 3, is greater than permitted 44: [04:48:24] non-ring atom 2 marked aromatic 44: [04:48:24] non-ring atom 2 marked aromatic 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 1 2 3 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 1 2 3 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 44: [04:48:24] Explicit valence for atom # 1 O, 3, is greater than permitted 44: [04:48:24] Explicit valence for atom # 4 F, 2, is greater than permitted 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 6 7 8 44: [04:48:24] Explicit valence for atom # 1 C, 5, is greater than permitted 44: [04:48:24] WARNING: not removing hydrogen atom with dummy atom neighbors 44: [04:48:24] WARNING: not removing hydrogen atom with dummy atom neighbors 44: [04:48:24] WARNING: not removing hydrogen atom with wedged bond 44: [04:48:24] WARNING: not removing hydrogen atom without neighbors 44: [04:48:24] WARNING: not removing hydrogen atom without neighbors 35: smi match: *C(*)(*)C=O *C(*)(*)C=O 35: smi match: CSC=O CSC=O 35: smi match: * * 35: smi match: O=CCl O=CCl 35: smi match: *** *** 35: smi match: *C=O *C=O 35: smi match: C[OH] C[OH] 35: smi match: C[OH] C[OH] 35: smi match: C[OH] C[OH] 35: smi match: C[OH] C[OH] 35: smi match: C[CH]=O C[CH]=O 35: smi match: *=* *=* 35: smi match: *C *C 35: smi match: C#C C#C 35: smi match: *[CH]C=C *[CH]C=C 35: smi match: cCC(=O)[OH] cCC(=O)[OH] 35: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 35: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] 35: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 35: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 35: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O 35: smi match: *N(*)C*=O *N(*)C*=O 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: ** ** 44: [04:48:24] WARNING: not removing hydrogen atom without neighbors 44: [04:48:24] WARNING: not removing hydrogen atom without neighbors 44: [04:48:24] Unreasonable formal charge on hydrogen # 0. 44: [04:48:24] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() 44: [04:48:24] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() 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 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: no atom 44: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: at 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: no owner 44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 44: Failed Expression: dp_mol 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: atom not associated with this molecule 44: Violation occurred on line 186 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: no atom 44: Violation occurred on line 385 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: at 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: no owner 44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 44: Failed Expression: dp_mol 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: atom not associated with this molecule 44: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: no atom 44: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: at 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: no owner 44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h 44: Failed Expression: dp_mol 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: atom not associated with this molecule 44: Violation occurred on line 393 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: null atom passed in 44: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: atom_pin 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: cannot take ownership of an atom which already has an owner 44: Violation occurred on line 408 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: cannot take ownership of an bond which already has an owner 44: Violation occurred on line 434 in file ./Code/GraphMol/ROMol.cpp 44: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 44: **** 44: 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 44: [04:48:24] WARNING: not removing hydrogen atom without neighbors 44: [04:48:24] Explicit valence for atom # 1 F greater than permitted 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: plain atoms have no Query 44: Violation occurred on line 610 in file ./Code/GraphMol/Atom.cpp 44: Failed Expression: 0 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: plain atoms have no Query 44: Violation occurred on line 615 in file ./Code/GraphMol/Atom.cpp 44: Failed Expression: 0 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: plain bonds have no Query 44: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp 44: Failed Expression: 0 44: **** 44: 44: [04:48:24] 44: 44: **** 44: Pre-condition Violation 44: plain bonds have no query 44: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp 44: Failed Expression: 0 44: **** 44: 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 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] 44: [04:48:24] Unusual charge on atom 0 number of radical electrons set to zero 44: [04:48:24] Unusual charge on atom 0 number of radical electrons set to zero 44: [04:48:24] Unusual charge on atom 0 number of radical electrons set to zero 44: [04:48:24] non-ring atom 0 marked aromatic 44: [04:48:24] non-ring atom 0 marked aromatic 44: [04:48:24] Explicit valence for atom # 1 C, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 9 C, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 3 N, 4, is greater than permitted 44: [04:48:24] Explicit valence for atom # 15 C, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 11 C, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 9 C, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 9 C, 5, is greater than permitted 44: [04:48:24] Explicit valence for atom # 9 C, 6, is greater than permitted 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 7 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 3 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 3 7 44: [04:48:24] Can't kekulize mol. Unkekulized atoms: 3 7 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 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 35: smi match: * * 35: smi match: C[SH] C[SH] 35: smi match: c[SH] c[SH] 35: smi match: NC(N)=S NC(N)=S 35: smi match: * * 35: smi match: ***** ***** 35: smi match: NC(N)=O NC(N)=O 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing sf.net issue 280. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing sf.net issue 285. 35: [04:48:24] done 35: [04:48:24] done 35: [04:48:24] done 35: [04:48:24] done 35: [04:48:24] done 35: [04:48:24] done 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing Github2441: Add RDProps interface to Conformers. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing Issue2510: Pickle Confs as double. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing Github #2465: Negative atom-map numbers cause depickling to fail. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing loading pickled mols with conformers 44: [04:48:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing conformer reading/writing options 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing property reading options 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing property reading options 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing boost::serialization integration 35: [04:48:24] done 35: [04:48:24] ------------------------------------- 35: [04:48:24] Testing github issue 6036 33/223 Test #35: graphmoltestPickler .................... Passed 0.39 sec test 45 Start 45: graphmolOrganometallicsCatch 45: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch 45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 34/223 Test #29: pyDistGeom ............................. Passed 0.57 sec test 46 Start 46: graphmolSGroupCatch 46: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch 46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 44: [04:48:24] Explicit valence for atom # 1 O, 3, is greater than permitted 44: [04:48:24] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 44: [04:48:24] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 44: [04:48:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 44: [04:48:24] 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: 35/223 Test #44: graphmolTestsCatch ..................... Passed 0.16 sec test 47 Start 47: graphmolAdjustQueryCatch 47: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch 47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 47: Test timeout computed to be: 1500 45: Randomness seeded to: 2696010456 45: =============================================================================== 45: All tests passed (62 assertions in 6 test cases) 45: 36/223 Test #45: graphmolOrganometallicsCatch ........... Passed 0.07 sec test 48 Start 48: chiralityTestsCatch 48: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch 48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 46: Randomness seeded to: 2032093144 46: =============================================================================== 46: All tests passed (120 assertions in 6 test cases) 46: 37/223 Test #46: graphmolSGroupCatch .................... Passed 0.07 sec test 49 Start 49: canonTestsCatch 49: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch 49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 49: Test timeout computed to be: 1500 4: dynamic RDAny:0.232198 s 4: static RDValue:0 s 48: Randomness seeded to: 79356591 48: [04:48:24] unable to set wavy bonds for double bonds: 3 49: Randomness seeded to: 1375255948 49: =============================================================================== 49: All tests passed (137 assertions in 7 test cases) 49: 38/223 Test #49: canonTestsCatch ........................ Passed 0.04 sec test 50 Start 50: moliteratorTestsCatch 50: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 47: Randomness seeded to: 1660957557 47: =============================================================================== 47: All tests passed (281 assertions in 10 test cases) 47: 48: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 48: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 39/223 Test #47: graphmolAdjustQueryCatch ............... Passed 0.11 sec test 51 Start 51: queryTestsCatch 51: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 50: Randomness seeded to: 1090794079 50: =============================================================================== 50: All tests passed (14 assertions in 4 test cases) 50: 48: [04:48:24] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 48: [04:48:24] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 48: [04:48:24] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored 48: [04:48:24] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored 48: [04:48:24] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 48: =============================================================================== 48: All tests passed (1845 assertions in 63 test cases) 48: 40/223 Test #48: chiralityTestsCatch .................... Passed 0.12 sec 41/223 Test #50: moliteratorTestsCatch .................. Passed 0.06 sec test 52 Start 52: molbundleTestsCatch 52: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/molbundleTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/GraphMol/pickleTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 27: ......[04:48:24] Molecule does not have explicit Hs. Consider calling AddHs() 27: [04:48:24] 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: 51: Randomness seeded to: 167404481 51: =============================================================================== 51: All tests passed (10 assertions in 1 test case) 51: 4: dynamic RDValue:0.033607 s 4: deleted! 4: [04:48:24] ------------------------------------- 4: [04:48:24] Testing String Pickle Roundtrips. 4: [04:48:24] done 4: [04:48:24] ------------------------------------- 4: [04:48:24] Testing conversion of vect to string. 4: [04:48:24] done 4: [04:48:24] ------------------------------------- 4: [04:48:24] Testing returning const references. 4: [04:48:24] any cast 4: [04:48:24] done: 0.000767 300000 4: [04:48:24] copy 4: [04:48:24] done: 0.000831 300000 4: [04:48:24] ref 4: [04:48:24] done: 0.000768 300000 4: [04:48:24] dict 4: [04:48:24] done: 0.001915 300000 4: [04:48:24] ref with hasVal 33: [04:48:24] Maximum BFS search size exceeded. 33: This is likely due to a highly symmetric fused ring system. 52: Randomness seeded to: 1782730244 52: =============================================================================== 52: All tests passed (6 assertions in 1 test case) 52: 42/223 Test #51: queryTestsCatch ........................ Passed 0.07 sec 43/223 Test #52: molbundleTestsCatch .................... Passed 0.04 sec test 54 Start 54: smiTest1 54: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 54: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 55: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 55: Test timeout computed to be: 1500 4: [04:48:24] done: 0.001266 300000 4: [04:48:24] done 4: [04:48:24] ------------------------------------- 4: [04:48:24] Testing dict update. 4: [04:48:24] done 4: deleted! 4: deleted! 4: deleted! 4: deleted! 4: deleted! 4: deleted! 53: Randomness seeded to: 3411788111 53: =============================================================================== 53: All tests passed (34 assertions in 1 test case) 53: 44/223 Test #4: testDict ............................... Passed 1.47 sec 45/223 Test #53: pickleTestsCatch ....................... Passed 0.07 sec test 56 Start 56: cxsmilesTest 56: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 56: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 57: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 55: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' 55: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 55: [04:48:24] SMILES Parse Error: syntax error while parsing: - 55: [04:48:24] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' 55: [04:48:24] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' 55: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' 55: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' 55: [04:48:24] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' 55: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' 55: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' 55: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' 55: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' 55: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' 55: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' 55: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] WARNING: not removing hydrogen atom without neighbors 54: [04:48:24] Invalid chiral specification on atom 0 54: [04:48:24] Invalid chiral specification on atom 0 54: [04:48:24] Invalid chiral specification on atom 0 54: [04:48:24] Invalid chiral specification on atom 0 54: [04:48:24] Invalid chiral specification on atom 0 54: [04:48:24] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' 54: [04:48:24] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 46/223 Test #55: smiTest2 ............................... Passed 0.07 sec test 58 Start 58: smiTestCatch 58: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 58: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 58: Randomness seeded to: 3011262604 58: [04:48:24] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 58: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 58: [04:48:24] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' 54: --C1CCC2(CC1)CCCCC2CCC1CCCC1 58: [04:48:24] SMARTS Parse Error: unclosed ring for input: 'C1C' 58: [04:48:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 58: [04:48:24] SMARTS Parse Error: syntax error while parsing: C)foo 58: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' 58: [04:48:24] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| 58: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 27: ... 27: ---------------------------------------------------------------------- 27: Ran 12 tests in 0.655s 27: 27: OK 58: [04:48:24] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' 54: smi: ClC1CCCCC1 54: smi: ClC1CCCCC1 54: smi: ClC1CCCCC1Br 54: smi: c1ccccc1 54: smi: c1ccncc1 54: smi: c1cc[nH]c1 54: smi: c1cc[nH]c1 54: smi: c1cc[pH]c1 54: CbC(aC)aC 54: CaC(bC)aC 54: CbC(bC)aC 54: O.C 54: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O 54: [04:48:24] SMILES Parse Error: syntax error while parsing: c%()ccccc%() 54: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' 54: [04:48:24] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) 54: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' 54: [04:48:24] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' 54: [04:48:24] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' 54: [04:48:24] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [04:48:24] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [04:48:24] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [04:48:24] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [04:48:24] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 54: [04:48:24] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# 54: [04:48:24] 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: [04:48:24] SMILES Parse Error: extra close parentheses while parsing: C) 54: [04:48:24] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' 47/223 Test #54: smiTest1 ............................... Passed 0.22 sec test 59 Start 59: nontetrahedralCatch 59: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 59: Randomness seeded to: 3981801346 59: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 57: [04:48:24] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC 57: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' 57: [04:48:24] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON 57: [04:48:24] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' 57: [04:48:24] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 57: [04:48:24] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 58: [04:48:24] w block attempts to set wedging on bond 0 more than once. 58: [04:48:24] improperly formatted w block 59: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: [04:48:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 58: [04:48:24] atom 3 is not associated with bond 1 in w block 48/223 Test #57: smaTest1 ............................... Passed 0.23 sec test 60 Start 60: testDepictor 60: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor 60: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 60: Test timeout computed to be: 1500 59: [04:48:24] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 59: =============================================================================== 59: All tests passed (308 assertions in 9 test cases) 59: 49/223 Test #59: nontetrahedralCatch .................... Passed 0.09 sec test 61 Start 61: depictorCatch 61: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch 61: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 61: Test timeout computed to be: 1500 58: =============================================================================== 58: All tests passed (1516 assertions in 53 test cases) 58: 50/223 Test #58: smiTestCatch ........................... Passed 0.24 sec 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-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap 62: Test timeout computed to be: 1500 51/223 Test #27: pyForceFieldConstraints ................ Passed 1.35 sec test 63 Start 63: testMrvToMol 63: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse 63: Test timeout computed to be: 1500 33: [04:48:24] Maximum BFS search size exceeded. 33: This is likely due to a highly symmetric fused ring system. 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 63: Using new chirality perception 63: Test 63: 63: NewChiralTest.sdf 63: 63: Test 63: 63: NewChiralTest.sdf 63: 63: Test 63: 63: NewChiralTestNoChiral.sdf 63: 63: Test 63: 63: NewChiralTestNoChiral.sdf 63: 63: Test 63: 63: NewChiralTestAllChiral.sdf 63: 63: Test 63: 63: NewChiralTestAllChiral.sdf 63: 63: Test 63: 63: ProblemShort.mol 63: 63: [04:48:24] For a MultipleSgroup expansion, the matching orphaned bond was not found 63: The multiple sgroup will be ignored 61: Randomness seeded to: 4241178033 61: =============================================================================== 61: All tests passed (571 assertions in 14 test cases) 61: 52/223 Test #33: graphmolMolOpsTest ..................... Passed 1.16 sec test 64 Start 64: fileParsersTest1 64: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 64: Test timeout computed to be: 1500 53/223 Test #61: depictorCatch .......................... Passed 0.19 sec test 65 Start 65: testMolSupplier 65: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 65: Test timeout computed to be: 1500 64: *************************************** 64: *************************************** 65: [04:48:25] 65: ----------------------------------------- 64: [04:48:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [04:48:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [04:48:25] bond with order 0 found on line 7. This is not part of the MDL specification. 64: [04:48:25] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 64: [04:48:25] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 64: [04:48:25] 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 65: [04:48:25] 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: 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 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: [04:48:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 63: [04:48:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 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: [04:48:25] 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 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 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 63: Test 63: 63: MarvinBadSruAtomRef.mrv 63: 63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 63: Test 63: 63: MarvinBadSruConnect.mrv 63: 63: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file 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 63: Test 63: 63: MarvinBadSupAttachOrder.mrv 63: 63: Order for an AttachmentPoint definition must be an integer in MRV file 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: 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: 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: MarvinBadSupMissingAttachBond.mrv 63: 63: No attachment point found for bond to the condensed atom in a superatomSgroup 63: Test 63: 63: MarvinBadSupMissingAttachOrder.mrv 63: 63: Expected atom, order and bond, for an AttachmentPoint definition in MRV file 60: [04:48:25] Warning: stereochemistry around double bond may be incorrect in depiction. 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: [04:48:25] initialization failed 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: 65: [04:48:25] Finished: testMolSup() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testRandMolSup() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 54/223 Test #63: testMrvToMol ........................... Passed 0.40 sec test 66 Start 66: testGeneralFileReader 66: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 66: Test timeout computed to be: 1500 55/223 Test #60: testDepictor ........................... Passed 0.48 sec test 67 Start 67: testMultithreadedMolSupplier 67: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 66: [04:48:25] 66: ----------------------------------------- 66: [04:48:25] Finished: testDetermineFormat() 66: [04:48:25] ----------------------------------------- 66: 66: [04:48:25] 66: ----------------------------------------- 65: [04:48:25] Finished: testSmilesSup() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] ------------------------------------------------------ 65: [04:48:25] SMILES Parse Error: syntax error while parsing: fail 65: [04:48:25] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 65: [04:48:25] ERROR: Smiles parse error on line 3 65: [04:48:25] ERROR: Cannot create molecule from : 'fail' 65: [04:48:25] ------------------------------------------------------ 65: [04:48:25] ------------------------------------------------------ 65: [04:48:25] >>> This may result in an infinite loop. It should finish almost immediately: 65: [04:48:25] <<< done. 65: [04:48:25] Finished: testSmilesSupFromText() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testSmilesWriter() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 67: [04:48:25] 67: ----------------------------------------- 65: [04:48:25] Finished: testSDWriter() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testSDSupplierEnding() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testSuppliersEmptyFile() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testCisTrans() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testStereoRound() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 65: [04:48:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 65: [04:48:25] Finished: testIssue226() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testTDTSupplier1() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testTDTSupplier2() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testTDTSupplier3() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testSDSupplierFromText() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] ERROR: Problems encountered parsing data fields 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] ERROR: Problems encountered parsing data fields 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Spurious data before the first property will be ignored 65: [04:48:25] Property will be truncated after the first blank line 65: [04:48:25] Property will be truncated after the first blank line 65: [04:48:25] Property will be truncated after the first blank line 65: [04:48:25] Finished: testSDSupplierStrLax1() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] ERROR: Problems encountered parsing data fields 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Property will be truncated after the first blank line 65: [04:48:25] Finished: testSDSupplierStrLax2() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] ERROR: Problems encountered parsing data fields 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] ERROR: Problems encountered parsing data fields 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Spurious data before the first property will be ignored 65: [04:48:25] Property will be truncated after the first blank line 65: [04:48:25] Property will be truncated after the first blank line 65: [04:48:25] Property will be truncated after the first blank line 65: [04:48:25] Finished: testSDSupplierFromTextStrLax1() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] ERROR: Problems encountered parsing data fields 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Property will be truncated after the first blank line 65: [04:48:25] Finished: testSDSupplierFromTextStrLax2() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testIssue265() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] ERROR: End of data field name not found 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Explicit valence for atom # 0 F, 2, is greater than permitted 65: [04:48:25] ERROR: Could not sanitize molecule ending on line 16 65: [04:48:25] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted 65: [04:48:25] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] ERROR: Bond line too short: 'M END' on line 18 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Finished: testSDErrorHandling() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testIssue381() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 66: [04:48:25] Finished: testSdf() 66: [04:48:25] ----------------------------------------- 66: 66: [04:48:25] 66: ----------------------------------------- 65: [04:48:25] Finished: testSetStreamIndices() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testMixIterAndRandom() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: build: 65: [04:48:25] Finished: testRemoveHs() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testGetItemText() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 66: [04:48:25] Finished: testSmi() 66: [04:48:25] ----------------------------------------- 66: 66: [04:48:25] 66: ----------------------------------------- 65: [04:48:25] Finished: testForwardSDSupplier() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testMissingCRSDSupplier() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testIssue3482695() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] ERROR: Cannot convert 'foo' to unsigned int on line 557 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Finished: testIssue3525673() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 56: Randomness seeded to: 4222970139 56: =============================================================================== 56: All tests passed (1902 assertions in 21 test cases) 56: 65: [04:48:25] Finished: testBlankLinesInProps() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testSkipLines() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testGitHub23() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testGitHub88() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 56/223 Test #56: cxsmilesTest ........................... Passed 0.89 sec test 68 Start 68: testMolWriter 68: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 68: Test timeout computed to be: 1500 65: [04:48:25] Finished: testGitHub2285() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 65: [04:48:25] ERROR: Smiles parse error on line 1 65: [04:48:25] ERROR: Cannot create molecule from : 'c1ccccc' 65: [04:48:25] SMILES Parse Error: extra open parentheses for input: 'C(C' 65: [04:48:25] ERROR: Smiles parse error on line 3 65: [04:48:25] ERROR: Cannot create molecule from : 'C(C' 65: [04:48:25] Explicit valence for atom # 1 C, 5, is greater than permitted 65: [04:48:25] ERROR: Could not sanitize molecule on line 5 65: [04:48:25] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 65: [04:48:25] Explicit valence for atom # 1 F, 2, is greater than permitted 65: [04:48:25] ERROR: Could not sanitize molecule ending on line 21 65: [04:48:25] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 65: [04:48:25] Explicit valence for atom # 1 F, 2, is greater than permitted 65: [04:48:25] ERROR: Could not sanitize molecule ending on line 21 65: [04:48:25] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 65: [04:48:25] Explicit valence for atom # 1 F, 2, is greater than permitted 65: [04:48:25] ERROR: Could not sanitize molecule ending on line 21 65: [04:48:25] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 65: [04:48:25] ERROR: Atom line too short: ' -9.6' on line 28 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Explicit valence for atom # 1 F, 2, is greater than permitted 65: [04:48:25] ERROR: Could not sanitize molecule ending on line 21 65: [04:48:25] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 65: [04:48:25] ERROR: Atom line too short: ' -9.6' on line 28 65: [04:48:25] ERROR: moving to the beginning of the next molecule 65: [04:48:25] Finished: testGitHub2479() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] 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: [04:48:25] Finished: testGitHub2881() 65: [04:48:25] ----------------------------------------- 65: 65: [04:48:25] ----------------------------------------- 65: [04:48:25] Finished: testGitHub3517() 65: [04:48:25] ----------------------------------------- 65: 57/223 Test #65: testMolSupplier ........................ Passed 0.46 sec test 69 Start 69: testTplParser 69: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 69: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 58/223 Test #69: testTplParser .......................... Passed 0.05 sec test 70 Start 70: testMol2ToMol 70: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 70: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 66: [04:48:25] Finished: testMae() 66: [04:48:25] ----------------------------------------- 66: 66: [04:48:25] 66: ----------------------------------------- 66: [04:48:25] Finished: testTdt() 66: [04:48:25] ----------------------------------------- 66: 59/223 Test #66: testGeneralFileReader .................. Passed 0.29 sec test 71 Start 71: testSequence 71: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence 71: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 60/223 Test #70: testMol2ToMol .......................... Passed 0.06 sec test 72 Start 72: testExtendedStereoParsing 72: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 72: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 72: Test timeout computed to be: 1500 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 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: 61/223 Test #71: testSequence ........................... Passed 0.10 sec 62/223 Test #72: testExtendedStereoParsing .............. Passed 0.06 sec test 73 Start 73: fileParsersCatchTest 73: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 74: Test timeout computed to be: 1500 73: Randomness seeded to: 2965640667 73: [04:48:25] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 73: [04:48:25] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 73: [04:48:25] Could not infer missing lvIdx on malformed SAP line for SGroup 1 73: [04:48:25] SGroup 1 is invalid and will be ignored 73: [04:48:25] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 73: [04:48:25] Could not infer missing lvIdx on malformed SAP line for SGroup 1 73: [04:48:25] SGroup 1 is invalid and will be ignored 73: [04:48:25] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 73: [04:48:25] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 73: [04:48:25] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 73: [04:48:25] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 73: [04:48:25] Could not infer missing lvIdx on malformed SAP line for SGroup 1 73: [04:48:25] SGroup 1 is invalid and will be ignored 73: [04:48:25] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 73: [04:48:25] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 73: [04:48:25] Could not infer missing lvIdx on malformed SAP line for SGroup 1 73: [04:48:25] SGroup 1 is invalid and will be ignored 73: [04:48:25] SGroup 3 referenced on line 40 not found. 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: no bonds 73: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp 73: Failed Expression: !d_bonds.empty() 73: **** 73: 73: [04:48:25] SGroup 3 referenced on line 40 not found. 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: no bonds 73: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp 73: Failed Expression: !d_bonds.empty() 73: **** 73: 73: [04:48:25] no bonds 73: [04:48:25] SGroup 1 is invalid and will be ignored 73: [04:48:25] SGroup line too short: 'M SBV 1 6' on line 42 73: [04:48:25] SGroup 1 is invalid and will be ignored 73: [04:48:25] SGroup line too short: 'M SBL 2 3 9 10' on line 46 73: [04:48:25] SGroup 2 is invalid and will be ignored 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [04:48:25] bookmark not found 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bond is not part of the SubstanceGroup 73: Violation occurred on line 158 in file ./Code/GraphMol/SubstanceGroup.cpp 73: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 73: **** 73: 73: [04:48:25] bond is not part of the SubstanceGroup 73: [04:48:25] SGroup 2 is invalid and will be ignored 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [04:48:25] bookmark not found 73: [04:48:25] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. 73: [04:48:25] SGroup 2 is invalid and will be ignored 73: [04:48:25] WARNING: final character of V3000 array is not ')' 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [04:48:25] WARNING: final character of V3000 array is not ')' 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [04:48:25] bookmark not found 73: [04:48:25] SGroup 1 is invalid and will be ignored 73: [04:48:25] WARNING: final character of V3000 array is not ')' 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [04:48:25] WARNING: final character of V3000 array is not ')' 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [04:48:25] bookmark not found 73: [04:48:25] SGroup 1 is invalid and will be ignored 73: [04:48:25] 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: 74: Randomness seeded to: 2177435270 74: =============================================================================== 74: All tests passed (95 assertions in 4 test cases) 74: 63/223 Test #74: testPropertyLists ...................... Passed 0.07 sec test 75 Start 75: XYZFileParserCatchTest 75: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: 73: [04:48:25] bookmark not found 73: [04:48:25] SGroup 2 is invalid and will be ignored 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: bookmark not found 73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: 73: [04:48:25] bookmark not found 73: [04:48:25] SGroup 2 is invalid and will be ignored 73: [04:48:25] Explicit valence for atom # 2 O, 3, is greater than permitted 73: [04:48:25] Explicit valence for atom # 1 O, 3, is greater than permitted 73: [04:48:25] Explicit valence for atom # 1 C, 5, is greater than permitted 26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 73: [04:48:25] sanitize [04:48:25] UNK: [04:48:25] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 75: Randomness seeded to: 2566735726 75: =============================================================================== 75: All tests passed (100 assertions in 2 test cases) 75: 64/223 Test #75: XYZFileParserCatchTest ................. Passed 0.04 sec test 76 Start 76: cdxmlParserCatchTest 76: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 76: Test timeout computed to be: 1500 73: [04:48:25] skipping block at line 7: 'BEGIN ATOM' 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 144 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp 73: Failed Expression: dp_inStream 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 179 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp 73: Failed Expression: dp_inStream 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 427 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp 73: Failed Expression: dp_inStream 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 274 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp 73: Failed Expression: dp_inStream 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Pre-condition Violation 73: no stream 73: Violation occurred on line 515 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 73: Failed Expression: dp_sInStream != nullptr 73: **** 73: 73: [04:48:25] Found a SCD/SED line with missing/empty SDT specification at line 21 73: [04:48:25] Found a SCD/SED line with missing/empty SDT specification at line 20 73: [04:48:25] 73: 73: **** 73: Post-condition Violation 73: Element '' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [04:48:25] BEGIN SGROUP line not found on line 14 73: [04:48:25] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. 73: [04:48:25] END SGROUP line not found on line 14 73: [04:48:25] END SGROUP line not found on line 14 73: [04:48:25] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. 73: [04:48:25] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. 73: [04:48:25] 73: 73: **** 73: Range Error 73: idx 73: Violation occurred on line 328 in file ./Code/GraphMol/ROMol.cpp 73: Failed Expression: 99 < 9 73: **** 73: 73: [04:48:25] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. 73: [04:48:25] Multiple ATTCHPT values for atom 2 on line 9 73: [04:48:25] Found a SCD/SED line with missing/empty SDT specification at line 12 73: [04:48:25] SMARTS Parse Error: syntax error while parsing: [#6;R 73: [04:48:25] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' 73: [04:48:25] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. 73: [04:48:25] Skipping empty SMARTS value for SMARTSQ. 73: [04:48:25] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. 73: [04:48:25] Found a SCD/SED line with missing/empty SDT specification at line 12 73: [04:48:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 73: [04:48:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 73: [04:48:25] WARNING: Skipping property bar because the value includes an illegal blank line 73: [04:48:25] WARNING: Skipping property baz because the value includes an illegal blank line 73: [04:48:25] WARNING: Skipping property bletch 73: nope because the name includes a newline 73: [04:48:25] WARNING: Skipping property bletch 73: nope2 because the name includes a newline 73: [04:48:25] 73: 73: **** 73: Post-condition Violation 73: Element 'QQQ' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Post-condition Violation 73: Element 'QQQ' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Post-condition Violation 73: Element 'QQQ' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [04:48:25] 73: 73: **** 73: Post-condition Violation 73: Element 'QQQ' not found 73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 73: Failed Expression: anum > -1 73: **** 73: 73: [04:48:25] atom 3 has a negative isotope value. line: 15 68: [04:48:25] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 68: [04:48:25] bond with order 0 found on line 11. This is not part of the MDL specification. 68: [04:48:25] bond with order 0 found on line 16. This is not part of the MDL specification. 73: [04:48:25] 73: 73: **** 73: Invariant Violation 73: bad prop value 73: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 73: Failed Expression: nSwaps < 2 73: **** 73: 73: [04:48:25] 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: 76: Randomness seeded to: 2975806640 76: [04:48:25] Invalid or missing fragment id from CDXML fragment, assigning new one... 76: [04:48:25] Explicit valence for atom # 3 N, 4, is greater than permitted 76: [04:48:25] CDXMLParser: failed sanitizing skipping fragment 32 76: [04:48:25] Bad bond in CDXML skipping fragment 58... 76: [04:48:25] Invalid or missing fragment id from CDXML fragment, assigning new one... 76: [04:48:25] Bad bond in CDXML skipping fragment 58... 26: All 191 tests passed 65/223 Test #68: testMolWriter .......................... Passed 0.44 sec test 77 Start 77: molfileStereoCatchTest 77: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest 77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] WARNING: not removing hydrogen atom without neighbors 76: [04:48:25] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. 76: [04:48:25] Incomplete atom labelling, cannot make bond 76: [04:48:25] Incomplete atom labelling, cannot make bond 77: Randomness seeded to: 3498580096 77: [04:48:25] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 77: [04:48:25] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 76: [04:48:25] Incomplete atom labelling, cannot make bond 77: [04:48:25] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 77: [04:48:25] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 77: [04:48:25] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored 77: =============================================================================== 77: All tests passed (142 assertions in 6 test cases) 77: 66/223 Test #77: molfileStereoCatchTest ................. Passed 0.09 sec test 78 Start 78: connectTheDotsTest 78: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 78: Test timeout computed to be: 1500 73: [04:48:25] ERROR: molecules without atoms cannot be exported to Maestro files. 73: [04:48:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 73: [04:48:25] ERROR: the mol cannot be kekulized, and will not be written to the output file. 73: [04:48:25] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. 76: [04:48:25] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 76: [04:48:25] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas 76: [04:48:25] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast 76: [04:48:25] Failed to parse XML fragment 5 node: b attribute: Order: 5 76: =============================================================================== 76: All tests passed (252 assertions in 4 test cases) 76: 26: 26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... 67/223 Test #76: cdxmlParserCatchTest ................... Passed 0.20 sec test 79 Start 79: testSubstructMatch 79: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 79: Test timeout computed to be: 1500 73: [04:48:25] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 73: [04:48:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 73: [04:48:25] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 73: [04:48:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 73: =============================================================================== 73: All tests passed (1311 assertions in 87 test cases) 73: 68/223 Test #73: fileParsersCatchTest ................... Passed 0.34 sec test 80 Start 80: substructTestCatch 80: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 80: Test timeout computed to be: 1500 78: Randomness seeded to: 869925510 78: =============================================================================== 78: All tests passed (8 assertions in 1 test case) 78: 79: ----------------- Test 1 79: Done 79: 79: ----------------- Test 2 79: Done 79: 79: ----------------- Test 3 79: Done 79: 79: ----------------- Test 4 79: Done 79: 79: ----------------- Test 5 79: Done 79: 79: ----------------- Test 5 QueryRoot 79: Done 79: 79: ----------------- Test 6 (Issue71 related) 79: Done 79: 79: ----------------- Testing serial numbers on recursive queries 79: Done 79: 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test multithreading 79: reading molecules 69/223 Test #78: connectTheDotsTest ..................... Passed 0.05 sec test 81 Start 81: testGenericGroups 81: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups 81: Test timeout computed to be: 1500 62: ..............[04:48:26] SMILES Parse Error: syntax error while parsing: invalidsmiles 62: [04:48:26] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' 79: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 79: processing 79: launch :0 79: launch :1 79: launch :2 79: launch :3 79: done 79: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 79: processing2 79: launch2 :0 79: launch2 :1 79: launch2 :2 79: launch2 :3 62: ..... 62: ---------------------------------------------------------------------- 62: Ran 19 tests in 0.734s 62: 62: OK 64: [04:48:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [04:48:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [04:48:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [04:48:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [04:48:26] deprecated group abbreviation ignored on line 24 81: Randomness seeded to: 1307232339 81: =============================================================================== 81: All tests passed (9408 assertions in 38 test cases) 81: 79: done 79: preprocessing 3 79: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 79: processing3 79: launch3 :0 79: launch3 :1 79: launch3 :2 79: launch3 :3 70/223 Test #81: testGenericGroups ...................... Passed 0.26 sec test 82 Start 82: testReaction 82: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 82: Test timeout computed to be: 1500 64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 64: [04:48:26] 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: 82: smi: O=C1CNC(=O)CN1 82: 1: O=C1CNC(=O)CN1 82: 2: COOC 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 82: [04:48:26] 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: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 4 79: done 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test GitHub issue 15 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test GitHub issue 409 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test chiral matching 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test GitHub issue 688: partially specified chiral substructure queries don't work properly 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test dative-bond matching 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test cis/trans matching 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test cis/trans matching part 2 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS 82: [04:48:26] atom 0 in product 0 has multiple charge specifications. 82: mass: 15.0001 82: Oc1ccccn1 82: Oc1ccc[nH]1 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] 82: [04:48:26] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: ([C:2] 82: [04:48:26] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] 82: [04:48:26] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: [C:2]) 82: [04:48:26] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' 79: [04:48:26] done 79: [04:48:26] ------------------------------------- 79: [04:48:26] Testing matching E/Z against Cis/Trans stereo bonds 79: [04:48:26] 79: 79: **** 79: Pre-condition Violation 79: matches must not be empty 79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 79: Failed Expression: !matches.empty() 79: **** 79: 79: [04:48:26] 79: 79: **** 79: Pre-condition Violation 79: matches must not be empty 79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 79: Failed Expression: !matches.empty() 79: **** 79: 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test substructure matching with a pathological case for symmetric SSSR 82: [04:48:26] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] 82: [04:48:26] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 82: [04:48:26] reactant 2 has no mapped atoms. 82: [04:48:26] >> Atoms within one molecule have different RXN roles. 82: [04:48:26] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] 82: [04:48:26] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: ([C:2] 82: [04:48:26] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) 82: [04:48:26] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' 82: [04:48:26] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] 82: [04:48:26] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' 82: [04:48:26] reactant 0 has no mapped atoms. 82: [04:48:26] reactant 1 has no mapped atoms. 82: [04:48:26] reactant 3 has no mapped atoms. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 5 found multiple times. 82: [04:48:26] product atom-mapping number 6 found multiple times. 82: [04:48:26] product atom-mapping number 7 found multiple times. 82: [04:48:26] product atom-mapping number 8 found multiple times. 82: [04:48:26] product atom-mapping number 12 found multiple times. 82: [04:48:26] product atom-mapping number 9 found multiple times. 82: [04:48:26] product atom-mapping number 10 found multiple times. 82: [04:48:26] product atom-mapping number 11 found multiple times. 82: [04:48:26] reactant 0 has no mapped atoms. 82: [04:48:26] reactant 1 has no mapped atoms. 82: [04:48:26] reactant 3 has no mapped atoms. 82: [04:48:26] reactant atom-mapping number 19 found multiple times. 82: [04:48:26] reactant atom-mapping number 25 found multiple times. 82: [04:48:26] reactant atom-mapping number 20 found multiple times. 82: [04:48:26] reactant atom-mapping number 21 found multiple times. 82: [04:48:26] reactant atom-mapping number 22 found multiple times. 82: [04:48:26] reactant atom-mapping number 23 found multiple times. 82: [04:48:26] reactant atom-mapping number 24 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 82: [04:48:26] product atom-mapping number 5 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 5 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br 82: [04:48:26] product atom-mapping number 5 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 5 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: F[C@@](Cl)(Br)O[C@](F)(Cl)Br 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: F[C@](Cl)(Br)O[C@](F)(Cl)Br 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 4 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 4 82: [04:48:26] product atom-mapping number 3 found multiple times. 82: [04:48:26] product atom-mapping number 2 found multiple times. 82: [04:48:26] product atom-mapping number 1 found multiple times. 82: [04:48:26] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 4 82: [04:48:26] product atom-mapping number 6 not found in reactants. 82: [04:48:26] product atom-mapping number 7 not found in reactants. 82: [04:48:26] product atom-mapping number 8 not found in reactants. 82: [04:48:26] product atom-mapping number 7 not found in reactants. 82: [04:48:26] product atom-mapping number 8 not found in reactants. 82: [04:48:26] product atom-mapping number 9 not found in reactants. 82: [04:48:26] product atom-mapping number 10 not found in reactants. 82: [04:48:26] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 6 82: [04:48:26] product atom-mapping number 7 not found in reactants. 82: [04:48:26] product atom-mapping number 8 not found in reactants. 82: [04:48:26] product atom-mapping number 9 not found in reactants. 82: [04:48:26] product atom-mapping number 10 not found in reactants. 82: [04:48:26] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 6 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] 79: [04:48:26] ------------------------------------- 79: [04:48:26] Test isAtomTerminalRGroupOrQueryHydrogen 71/223 Test #79: testSubstructMatch ..................... Passed 0.39 sec test 83 Start 83: testReactionFingerprints 83: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 83: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 83: Test timeout computed to be: 1500 82: [04:48:26] 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 83: [04:48:26] ------------------------------------- 83: [04:48:26] Test Reaction StructuralFingerprint 72/223 Test #62: pyDepictor ............................. Passed 1.57 sec test 84 Start 84: testEnumeration 84: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 84: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 84: Test timeout computed to be: 1500 83: [04:48:26] ------------------------------------- 83: [04:48:26] Test Reaction DifferenceFingerprint 82: [04:48:26] product atom-mapping number 17 not found in reactants. 82: [04:48:26] product atom-mapping number 18 not found in reactants. 82: [04:48:26] mapped atoms in the reactants were not mapped in the products. 82: unmapped numbers are: 12 73/223 Test #83: testReactionFingerprints ............... Passed 0.06 sec test 85 Start 85: rxnTestCatch 85: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 85: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 85: Test timeout computed to be: 1500 82: [04:48:26] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 82: [04:48:26] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 82: 82: [04:48:26] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 82: ------------- 82: CCOc1ccccc1 85: Randomness seeded to: 3052906313 85: [04:48:26] atom 0 in product 0 has multiple charge specifications. 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 34 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 36 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 38 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 40 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 42 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 87 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 89 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 91 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 93 85: [04:48:26] Found a SCD/SED line with missing/empty SDT specification at line 95 85: [04:48:26] mapped atoms in the reactants were not mapped in the products. 85: unmapped numbers are: 2 85: [04:48:26] mapped atoms in the reactants were not mapped in the products. 85: unmapped numbers are: 2 85: [04:48:26] SMARTS Parse Error: unclosed ring for input: 'CC1' 85: [04:48:26] SMILES Parse Error: unclosed ring for input: 'CC1' 85: [04:48:26] mapped atoms in the reactants were not mapped in the products. 85: unmapped numbers are: 2 85: [04:48:26] product atom-mapping number 2 not found in reactants. 85: [04:48:26] mapped atoms in the reactants were not mapped in the products. 85: unmapped numbers are: 2 84: 30000000 30000000 82: [04:48:26] reactant 0 has no mapped atoms. 82: [04:48:26] product 0 has no mapped atoms. 82: [04:48:26] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. 85: [04:48:26] product atom-mapping number 2 not found in reactants. 85: [04:48:26] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 74/223 Test #82: testReaction ........................... Passed 0.28 sec test 86 Start 86: pyChemReactions 86: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 86: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 86: Test timeout computed to be: 1500 85: =============================================================================== 85: All tests passed (568 assertions in 20 test cases) 85: 75/223 Test #85: rxnTestCatch ........................... Passed 0.15 sec test 87 Start 87: pyChemReactionEnumerations 87: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 87: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 87: Test timeout computed to be: 1500 80: Randomness seeded to: 1115563814 80: =============================================================================== 80: All tests passed (143 assertions in 7 test cases) 80: 76/223 Test #80: substructTestCatch ..................... Passed 0.64 sec test 88 Start 88: pyChemReactionSanitize 88: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 88: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 88: Test timeout computed to be: 1500 87: [04:48:27] == testCartesianProduct 87: .[04:48:27] == testEnumerateLibrary 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 86: [04:48:27] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 86: [04:48:27] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 86: .[04:48:27] 86: 86: **** 86: Pre-condition Violation 86: getNumImplicitHs() called without preceding call to calcImplicitValence() 86: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp 86: Failed Expression: d_implicitValence > -1 86: **** 86: 86: [04:48:27] 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: 87: ..[04:48:27] == testRGroupState 86: .......[04:48:27] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 86: [04:48:27] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 86: [04:48:27] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 86: [04:48:27] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) 86: .[04:48:27] product atom-mapping number 1 found multiple times. 86: [04:48:27] product atom-mapping number 1 found multiple times. 87: .[04:48:27] == testRandomEnumerateAllBBsLibrary 87: ** [1, 1] 87: ** [0, 2] 87: ** [1, 0] 86: ................[04:48:27] mapped atoms in the reactants were not mapped in the products. 86: unmapped numbers are: 3 86: [04:48:27] mapped atoms in the reactants were not mapped in the products. 86: unmapped numbers are: 3 87: .[04:48:27] == testRandomEnumerateLibrary 87: .[04:48:27] == testRandomSample 86: .[04:48:27] mapped atoms in the reactants were not mapped in the products. 86: unmapped numbers are: 3 86: ..[04:48:27] reactant 2 has no mapped atoms. 86: [04:48:27] reactant 2 has no mapped atoms. 86: [04:48:27] product 1 has no mapped atoms. 86: ........[04:48:27] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q 86: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' 86: [04:48:27] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q 86: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' 86: .[04:48:27] reactant atom-mapping number 1 found multiple times. 86: [04:48:27] product atom-mapping number 2 not found in reactants. 86: [04:48:27] mapped atoms in the reactants were not mapped in the products. 86: unmapped numbers are: 4 86: [04:48:27] product atom-mapping number 5 not found in reactants. 87: .[04:48:27] == testRandomSampleAllBBs 87: .[04:48:27] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 87: [04:48:27] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 87: .[04:48:27] == testRemoveBadMatches 87: .[04:48:27] == testTimings 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: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 34 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 36 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 38 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 40 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 42 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 87 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 89 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 91 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 93 86: [04:48:27] Found a SCD/SED line with missing/empty SDT specification at line 95 88: .[04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 86: ..[04:48:27] SMARTS Parse Error: syntax error while parsing: boromicacid 86: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 86: [04:48:27] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 86: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 86: [04:48:27] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 86: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 88: .[04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] 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: [04:48:27] reactant 0 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] product 0 has no mapped atoms. 88: [04:48:27] Could not find RLabel mapping for atom: 0 in template: 1 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: [04:48:27] reactant 1 has no mapped atoms. 88: .. 88: ---------------------------------------------------------------------- 88: Ran 4 tests in 0.053s 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: [04:48:27] reaction has no reactants 86: [04:48:27] reaction has no products 86: [04:48:27] initialization failed 86: [04:48:27] reaction has no reactants 86: [04:48:27] reaction has no products 86: .[04:48:27] SMARTS Parse Error: syntax error while parsing: boromicacid 86: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 86: [04:48:27] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 86: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 86: [04:48:27] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 86: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 86: [04:48:27] reaction has no reactants 86: [04:48:27] reaction has no products 86: [04:48:27] initialization failed 86: [04:48:27] reaction has no reactants 86: [04:48:27] reaction has no products 86: . 86: ---------------------------------------------------------------------- 86: Ran 50 tests in 0.228s 86: 86: OK 86: ******************************************** 86: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn 86: 77/223 Test #88: pyChemReactionSanitize ................. Passed 1.06 sec test 89 Start 89: testChemTransforms 89: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 89: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 89: Test timeout computed to be: 1500 78/223 Test #38: hanoiTest .............................. Passed 3.75 sec 79/223 Test #86: pyChemReactions ........................ Passed 1.16 sec test 90 Start 90: chemTransformsTestCatch 90: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 90: Test timeout computed to be: 1500 test 91 Start 91: tautomerQueryTestCatch 91: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 91: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery 91: Test timeout computed to be: 1500 89: 1 smi: CC 89: 1 smi: CC 89: 2 smi: CCO[C@H](N)P 89: 2 smi: CC 89: replaceSub smi1:CCP(CC)[C@@H](N)O 89: replaceSub smi1:CCNCC 89: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 89: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O 89: [04:48:27] SMARTS Parse Error: syntax error while parsing: bar 89: [04:48:27] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' 90: Randomness seeded to: 2354015691 90: [04:48:27] Incomplete atom labelling, cannot make bond 90: [04:48:27] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 90: [04:48:27] Incomplete atom labelling, cannot make bond 90: [04:48:27] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 90: [04:48:27] Incomplete atom labelling, cannot make bond 90: [04:48:27] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 90: [04:48:27] Incomplete atom labelling, cannot make bond 90: [04:48:27] Incomplete atom labelling, cannot make bond 90: [04:48:27] Incomplete atom labelling, cannot make bond 90: [04:48:27] 90: 90: **** 90: Invariant Violation 90: molzip: bond info already exists for end atom with label:1 90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: !bond.b 90: **** 90: 90: [04:48:27] Incomplete atom labelling, cannot make bond 90: [04:48:27] 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: 80/223 Test #89: testChemTransforms ..................... Passed 0.12 sec test 92 Start 92: pyTautomerQuery 92: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 92: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 92: Test timeout computed to be: 1500 90: [04:48:27] 90: 90: **** 90: Invariant Violation 90: molzip: zipped Bond already exists, perhaps labels are duplicated 90: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp 90: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) 90: **** 90: 90: =============================================================================== 90: All tests passed (667 assertions in 7 test cases) 90: 81/223 Test #90: chemTransformsTestCatch ................ Passed 0.12 sec test 93 Start 93: testSubgraphs1 93: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 93: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 93: Test timeout computed to be: 1500 93: ----------------------- 93: Subgraph retrieval 93: Finished 93: ----------------------- 93: testSubgraphs2a 93: Finished 93: ----------------------- 93: testSubgraphs2 93: Finished 93: ----------------------- 93: Path retrieval 93: Finished 93: ----------------------- 93: Path retrieval2 93: Finished 93: ----------------------- 93: Unique Subgraph retrieval 93: Finished 93: ----------------------- 93: testUniqueSubgraphs2 92: ..... 92: ---------------------------------------------------------------------- 92: Ran 5 tests in 0.025s 92: 92: OK 87: . 87: ---------------------------------------------------------------------- 87: Ran 11 tests in 0.876s 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 0.05103778839111328 seconds 87: Skipped 10000000 in 0.3329131603240967 seconds 87: Skipped 10000000 in 0.14606189727783203 seconds 91: Randomness seeded to: 1295940423 91: =============================================================================== 91: All tests passed (93 assertions in 13 test cases) 91: 82/223 Test #91: tautomerQueryTestCatch ................. Passed 0.36 sec test 94 Start 94: testSubgraphs2 94: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 94: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 94: Test timeout computed to be: 1500 94: ----------------------- 94: Test1: pathToSubmol 83/223 Test #92: pyTautomerQuery ........................ Passed 0.32 sec test 95 Start 95: subgraphsCatch 95: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 95: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 95: Test timeout computed to be: 1500 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 93: Finished 93: ----------------------- 93: testRootedSubgraphs 93: Finished 93: ----------------------- 93: testRootedPaths 93: Finished 84/223 Test #93: testSubgraphs1 ......................... Passed 0.32 sec 85/223 Test #94: testSubgraphs2 ......................... Passed 0.06 sec test 96 Start 96: filterCatalogTest 96: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog 96: Test timeout computed to be: 1500 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-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 97: Test timeout computed to be: 1500 12: .................. 12: ---------------------------------------------------------------------- 12: Ran 18 tests in 4.531s 12: 12: OK 95: Randomness seeded to: 947667507 95: --------- 95: =============================================================================== 95: All tests passed (11 assertions in 1 test case) 95: 86/223 Test #95: subgraphsCatch ......................... Passed 0.07 sec test 98 Start 98: testFragCatalog 98: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog 98: Test timeout computed to be: 1500 87/223 Test #87: pyChemReactionEnumerations ............. Passed 1.64 sec test 99 Start 99: pyFragCatalog 99: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 99: Test timeout computed to be: 1500 98: 21 96: Warning: molecule failed filter 96: Warning: molecule failed filter: reason hzone_phenol_A(479) 96: v = { 96: 0,23}, 96: 1,22}, 96: 2,20}, 96: 3,19}, 96: 4,25}, 96: 5,24}, 96: 6,18}, 96: 7,17}, 96: 8,16}, 96: 9,21}, 96: } 96: match = { 96: 0,23}, 96: 1,22}, 96: 2,20}, 96: 3,19}, 96: 4,25}, 96: 5,24}, 96: 6,18}, 96: 7,17}, 96: 8,16}, 96: 9,21}, 96: } 96: Warning: molecule failed filter 96: Warning: molecule failed filter: reason cyano_imine_B(17) 96: v = { 96: 0,11}, 96: 1,12}, 96: 2,13}, 96: 3,14}, 96: 4,15}, 96: 5,10}, 96: 6,9}, 96: 7,8}, 96: 8,7}, 96: 9,6}, 96: 10,5}, 96: 11,17}, 96: 12,16}, 96: } 96: match = { 96: 0,11}, 96: 1,12}, 96: 2,13}, 96: 3,14}, 96: 4,15}, 96: 5,10}, 96: 6,9}, 96: 7,8}, 96: 8,7}, 96: 9,6}, 96: 10,5}, 96: 11,17}, 96: 12,16}, 96: } 96: Warning: molecule failed filter 96: Warning: molecule failed filter: reason keto_keto_gamma(5) 96: v = { 96: 0,0}, 96: 1,1}, 96: 2,2}, 96: 3,4}, 96: 4,5}, 96: 5,6}, 96: 6,7}, 96: 7,8}, 96: 8,9}, 96: 9,14}, 96: 10,15}, 96: 11,16}, 96: } 96: match = { 96: 0,0}, 96: 1,1}, 96: 2,2}, 96: 3,4}, 96: 4,5}, 96: 5,6}, 96: 6,7}, 96: 7,8}, 96: 8,9}, 96: 9,14}, 96: 10,15}, 96: 11,16}, 96: } 26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 88/223 Test #12: pyBV ................................... Passed 5.11 sec test 100 Start 100: testDescriptors 100: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 100: Test timeout computed to be: 1500 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test Crippen parameter acquisition. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test Crippen calculation. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test Issue262: problems with Crippen calculation from pickles. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test AMW calculation. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test Exact MW calculation. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test Labute ASA descriptors. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test TPSA descriptors. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test Lipinski parameters. 26: All 191 tests passed 89/223 Test #96: filterCatalogTest ...................... Passed 0.39 sec test 101 Start 101: testAUTOCORR2D 101: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 101: [04:48:28] ---------------------------- 101: start test autocorr2D 26: 26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test VSA descriptors. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test molecular formula calculation. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test Issue 3415534. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test Issue3433771: Bad definition for Crippen atom type O11. 100: [04:48:28] done 100: [04:48:28] ------------------------------------- 100: [04:48:28] Test multithreading 100: reading molecules 100: processing 100: launch :0 100: launch :1 100: launch :2 100: launch :3 98: [04:48:28] 98: 98: **** 98: Invariant Violation 98: nonsense 98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 98: Failed Expression: token != tokens.end() 98: **** 98: 98: [04:48:28] 98: 98: **** 98: Invariant Violation 98: nonsense no new line 98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 98: Failed Expression: token != tokens.end() 98: **** 98: 98: [04:48:28] 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: 90/223 Test #98: testFragCatalog ........................ Passed 0.56 sec test 102 Start 102: testATF 102: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF 102: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 99: ......... 99: ---------------------------------------------------------------------- 99: Ran 9 tests in 0.080s 99: 99: OK 91/223 Test #40: resMolSupplierTest ..................... Passed 4.81 sec test 103 Start 103: testBCUT 103: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 92/223 Test #102: testATF ................................ Passed 0.06 sec test 104 Start 104: testEEM 104: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM 104: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 104: Test timeout computed to be: 1500 103: [04:48:28] ------------------------------------- 103: [04:48:28] Basic BCUT tests. 103: [04:48:28] done 103: [04:48:28] ------------------------------------- 103: [04:48:28] Larger BCUT tests. 104: =>start test EEM 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: 0 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 93/223 Test #99: pyFragCatalog .......................... Passed 0.71 sec test 105 Start 105: testPBF 105: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF 105: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 105: Test timeout computed to be: 1500 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 105: [04:48:28] ------------------------------------- 105: [04:48:28] Basic PBF tests. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 101: [04:48:29] done 101: [04:48:29] ------------------------------------- 101: [04:48:29] Test Github #3806: NaNs from AUTOCORR2D descriptor 101: [04:48:29] done 94/223 Test #101: testAUTOCORR2D ......................... Passed 0.52 sec test 106 Start 106: testRDFcustom 106: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 106: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 106: Test timeout computed to be: 1500 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: 100 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: 200 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 105: [04:48:29] done 105: [04:48:29] ------------------------------------- 105: [04:48:29] PBF edge cases. 105: [04:48:29] done 95/223 Test #105: testPBF ................................ Passed 0.36 sec test 107 Start 107: testRDF 107: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF 107: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 107: Test timeout computed to be: 1500 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: 300 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: [04:48:29] ------------------------------------- 103: [04:48:29] Test empty molecule BCUT. 96/223 Test #103: testBCUT ............................... Passed 0.72 sec test 108 Start 108: testMORSE 108: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 108: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 108: Test timeout computed to be: 1500 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: 400 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: [04:48:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 104: Elapsed time: 0.824976 s 104: Errors:0 104: [04:48:29] test on : 500 molecules done 97/223 Test #104: testEEM ................................ Passed 0.88 sec test 109 Start 109: test3D 109: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 109: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 109: Test timeout computed to be: 1500 106: =>start test rdf custom 106: [04:48:29] test on : 365 molecules done 109: [04:48:29] ------------------------------------- 109: [04:48:29] Basic PMI tests. 109: [04:48:29] done 109: [04:48:29] ------------------------------------- 109: [04:48:29] More PMI/NPR tests. 109: [04:48:29] done 109: [04:48:29] ------------------------------------- 109: [04:48:29] Basic NPR tests. 97: .............[04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 97: [04:48:30] SMILES Parse Error: syntax error while parsing: --- 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' 97: [04:48:30] dasfsadf 107: =>start test rdf 107: [04:48:30] test on : 365 molecules done 98/223 Test #107: testRDF ................................ Passed 0.80 sec test 110 Start 110: testWHIM 110: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 110: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 110: Test timeout computed to be: 1500 97: .[04:48:30] SMILES Parse Error: syntax error while parsing: mydoghasfleas 97: [04:48:30] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' 109: [04:48:30] done 109: [04:48:30] ------------------------------------- 109: [04:48:30] PMI edge cases. 109: [04:48:30] done 109: [04:48:30] ------------------------------------- 109: [04:48:30] NPR edge cases. 109: [04:48:30] done 109: [04:48:30] ------------------------------------- 109: [04:48:30] 3D descriptors. 109: [04:48:30] done 109: [04:48:30] ------------------------------------- 109: [04:48:30] 3D descriptor edge cases. 109: [04:48:30] done 109: [04:48:30] ------------------------------------- 109: [04:48:30] Inertial shape factor. 109: [04:48:30] done 99/223 Test #109: test3D ................................. Passed 0.51 sec test 111 Start 111: testGETAWAY 111: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 111: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 97: ....... 97: ---------------------------------------------------------------------- 97: Ran 21 tests in 1.535s 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 106: =>start test morse custom 106: [04:48:30] test on : 365 molecules done 100/223 Test #97: pyFilterCatalog ........................ Passed 2.28 sec test 112 Start 112: testAUTOCORR3D 112: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 112: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 110: =>start test WHIM 110: [04:48:30] test on : 365 molecules done 101/223 Test #110: testWHIM ............................... Passed 0.40 sec test 113 Start 113: testCoulombMat 113: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 113: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 113: ===================== Testing CoulombMat ======================= 113: CM test 1 mat Done 102/223 Test #113: testCoulombMat ......................... Passed 0.05 sec test 114 Start 114: descriptorsTestCatch 114: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 114: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 114: Test timeout computed to be: 1500 114: Randomness seeded to: 2280435093 114: =============================================================================== 114: All tests passed (482 assertions in 7 test cases) 114: 103/223 Test #114: descriptorsTestCatch ................... Passed 0.07 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-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 115: Test timeout computed to be: 1500 64: [04:48:30] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 64: [04:48:30] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 108: =>start test MORSE 108: =>read file 108: [04:48:30] test on : 365 molecules done 104/223 Test #108: testMORSE .............................. Passed 1.28 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-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 116: Test timeout computed to be: 1500 64: ---------------------------------- 64: ---------------------------------- 64: [04:48:30] 64: 64: **** 64: Pre-condition Violation 64: rlabel out of range for MDL files 64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp 64: Failed Expression: rlabel >= 0 && rlabel < 100 64: **** 64: 64: [04:48:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 112: =>start test autocorr3D 112: [04:48:30] test on : 365 molecules done 105/223 Test #112: testAUTOCORR3D ......................... Passed 0.46 sec test 117 Start 117: testFingerprints 117: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 117: Test timeout computed to be: 1500 106: =>start test AUTOCORR3D custom 106: [04:48:30] test on : 365 molecules done 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: 0 117: 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: 0 117: 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: 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?: 0 117: 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: 0 117: 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 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?: 0 117: 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: ------------------- 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: ------------------- 117: 117: 117: 117: 117: 117: 117: 117: 117: 117: ------------------- 117: 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Morgan Fingerprints. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Morgan Fingerprints using fromAtoms argument. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Morgan Fingerprints as bit vects. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Morgan Fingerprints with feature invariants. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test additional Morgan fingerprints options. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Atom Codes. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Atom Pairs. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Atom Pairs part 2. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Topological Torsions. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Bulk Topological Torsions. 67: [04:48:31] Finished: testSmiCorrectness() 67: [04:48:31] ----------------------------------------- 67: 67: [04:48:31] 67: ----------------------------------------- 64: [04:48:31] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 64: [04:48:31] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Hashed Atom Pairs. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Hashed torsions. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Rooted Atom Pairs. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test ignoring atoms in Atom Pairs. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Rooted Topological Torsions. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test ignoring atoms in Topological Torsions. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test atom info from morgan fingerprints. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test atom info from morgan fingerprints including Info Redundant Environments. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] ------------------------------------- 117: [04:48:31] ------------------------------------- 67: [04:48:31] Spurious data before the first property will be ignored 67: [04:48:31] Property will be truncated after the first blank line 67: [04:48:31] Property will be truncated after the first blank line 67: [04:48:31] Property will be truncated after the first blank line 117: [04:48:31] ------------------------------------- 117: [04:48:31] ------------------------------------- 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Atom Pairs including info about chirality. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test Topological Torsions including info about chirality. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test GitHub Issue 25: fingerprint backwards compatibility. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test GitHub Issue 151: PatternFingerprint problems 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test 3D atom pairs. 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule 117: [04:48:31] done 117: [04:48:31] ------------------------------------- 117: [04:48:31] Test multithreading with the pattern FP 117: reading molecules 64: [04:48:31] Empty atom list: 'M ALS 1 0 F' on line 8. 64: de_DE.UTF-8 64: [04:48:31] ------------------------------------- 64: [04:48:31] Test multithreading Locale Switching 117: pass 1 117: launch :0 117: launch :1 117: launch :2 117: launch :3 106: =>start test 2 WHIM custom 106: [04:48:31] test on : 365 molecules done 115: .....[04:48:31] 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: 115: ......................... 115: ---------------------------------------------------------------------- 115: Ran 30 tests in 0.025s 115: 115: OK 115: exactmw 78.046950192 115: amw 78.11399999999999 115: lipinskiHBA 0.0 115: lipinskiHBD 0.0 115: NumRotatableBonds 0.0 115: NumHBD 0.0 115: NumHBA 0.0 115: NumHeavyAtoms 6.0 115: NumAtoms 6.0 115: NumHeteroatoms 0.0 115: NumAmideBonds 0.0 115: FractionCSP3 0.0 115: NumRings 1.0 115: NumAromaticRings 1.0 115: NumAliphaticRings 0.0 115: NumSaturatedRings 0.0 115: NumHeterocycles 0.0 115: NumAromaticHeterocycles 0.0 115: NumSaturatedHeterocycles 0.0 115: NumAliphaticHeterocycles 0.0 115: NumSpiroAtoms 0.0 115: NumBridgeheadAtoms 0.0 115: NumAtomStereoCenters 0.0 115: NumUnspecifiedAtomStereoCenters 0.0 115: labuteASA 37.43140311949697 115: tpsa 0.0 115: CrippenClogP 1.6866 115: CrippenMR 26.441999999999993 115: chi0v 3.464101615137755 115: chi1v 2.0000000000000004 115: chi2v 0.6666666666666671 115: chi3v 0.6666666666666671 115: chi4v 0.38490017945975075 115: chi0n 3.464101615137755 115: chi1n 2.0000000000000004 115: chi2n 0.6666666666666671 115: chi3n 0.6666666666666671 115: chi4n 0.38490017945975075 115: hallKierAlpha -0.78 115: kappa1 3.4115708812260532 115: kappa2 1.6057694396735218 115: kappa3 0.5823992601400448 115: Phi 0.9130327103921437 115: exactmw 78.046950192 115: lipinskiHBA 0.0 64: [04:48:31] Test multithreading (Done) 64: [04:48:31] ------------------------------------- 106/223 Test #115: pyMolDescriptors ....................... Passed 0.82 sec test 118 Start 118: testMHFPFingerprint 118: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 118: Test timeout computed to be: 1500 64: *************************************** 64: *************************************** 118: [04:48:31] ------------------------------------- 118: [04:48:31] Test MHFP fingerprint encoder initialization 64: [04:48:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 64: [04:48:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 118: [04:48:31] done 118: [04:48:31] ------------------------------------- 118: [04:48:31] Test MHFP shingling creation 64: [04:48:31] bond with order 0 found on line 7. This is not part of the MDL specification. 118: [04:48:31] done 118: [04:48:31] ------------------------------------- 118: [04:48:31] Test MHFP hashing of string and uint arrays 118: [04:48:31] done 118: [04:48:31] ------------------------------------- 118: [04:48:31] Test SECFP fingerprint functionality 118: [04:48:31] done 107/223 Test #118: testMHFPFingerprint .................... Passed 0.06 sec test 119 Start 119: testFingerprintGenerators 119: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 119: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 119: Test timeout computed to be: 1500 64: [04:48:31] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 64: [04:48:31] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) 64: [04:48:31] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test atom-pair fp generator 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test atom-pair fp generator with different arguments 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation 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 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test atom-pair additional output 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Folded Atom Pairs. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Rooted Atom Pairs. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test ignoring atoms in Atom Pairs. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Atom Pairs including info about chirality. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Morgan Fingerprints. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test morgan fp generator 64: check isomorphism 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Morgan Fingerprints using fromAtoms argument. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Morgan Fingerprints as bit vects. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Morgan Fingerprints with feature invariants. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test additional Morgan fingerprints options. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Single atoms setting radius 1 bits in Morgan fingerprints 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test different invariant generator combinations 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test invariant overriding 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test RDKit fp generator 67: [04:48:31] Finished: testSDCorrectness() 67: [04:48:31] ----------------------------------------- 67: 108/223 Test #67: testMultithreadedMolSupplier ........... Passed 6.31 sec test 120 Start 120: fpTestCatch 120: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 120: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 120: Test timeout computed to be: 1500 117: pass 2 117: launch :0 117: launch :1 117: launch :2 117: launch :3 120: Randomness seeded to: 2633254191 120: =============================================================================== 120: All tests passed (166 assertions in 14 test cases) 120: 109/223 Test #120: fpTestCatch ............................ Passed 0.08 sec test 121 Start 121: fpGenTestCatch 121: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 121: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 121: Test timeout computed to be: 1500 106: =>start test 1 WHIM custom 106: [04:48:31] test on : 365 molecules done 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test unfolded version of RDKFP 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test topological torsion fp generator 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Topological Torsions. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Folded torsions. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Bulk Topological Torsions. 116: ........ 116: ---------------------------------------------------------------------- 116: Ran 8 tests in 0.353s 116: 116: OK 121: Randomness seeded to: 2156604168 121: =============================================================================== 121: All tests passed (2678 assertions in 4 test cases) 121: 110/223 Test #121: fpGenTestCatch ......................... Passed 0.26 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-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 122: Test timeout computed to be: 1500 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Rooted Topological Torsions. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test ignoring atoms in Topological Torsions. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test Topological Torsions including info about chirality. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test GitHub Issue 25: fingerprint backwards compatibility. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 119: [04:48:31] done 119: [04:48:31] ------------------------------------- 119: [04:48:31] Test convenience and bulk fp calculation functions 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test Issue252: Bad definitions for Crippen atom types. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test calculation of ChiVs. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test calculation of ChiNs. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test calculation of HallKierAlpha. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test calculation of Kappa1. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test calculation of Kappa2. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test calculation of Kappa3. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test Crippen atom type calculations. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test ring descriptors 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test other count descriptors. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test MQN 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test GitHub Issue 56. 100: [04:48:32] WARNING: not removing hydrogen atom without neighbors 100: [04:48:32] WARNING: not removing hydrogen atom without neighbors 100: [04:48:32] WARNING: not removing hydrogen atom without neighbors 100: [04:48:32] WARNING: not removing hydrogen atom without neighbors 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test Github92: Bad Crippen atom type for pyrrole H. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test Github362: order dependence in Kier-Hall descriptors. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test calculation of spiro and bridgehead counts. 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test Github694: ExactMolWt ignoring the mass of the electron 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Testing Properties and KitchenSink 100: [04:48:32] ---Caught keyerror (bad property name)--- 100: [04:48:32] ---Caught stereo value error--- 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test USR Descriptor 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test Github #1973: support P and S terms for TPSA calculation 100: [04:48:32] done 100: [04:48:32] ------------------------------------- 100: [04:48:32] Test Github #2948: Empty molecule has non-zero LabuteASA 100: [04:48:32] done 111/223 Test #100: testDescriptors ........................ Passed 3.76 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-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 123: Test timeout computed to be: 1500 112/223 Test #116: pyMolDescriptors3D ..................... Passed 1.36 sec test 124 Start 124: testPartialCharges 124: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 124: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 124: Test timeout computed to be: 1500 113/223 Test #124: testPartialCharges ..................... Passed 0.05 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-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 125: Test timeout computed to be: 1500 119: [04:48:32] done 119: [04:48:32] ------------------------------------- 119: [04:48:32] Test GitHub Issue #6958 114/223 Test #119: testFingerprintGenerators .............. Passed 0.79 sec test 126 Start 126: testMolTransforms 126: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 126: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 126: Test timeout computed to be: 1500 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: *********************************************************** 115/223 Test #126: testMolTransforms ...................... Passed 0.05 sec test 127 Start 127: pyMolTransforms 127: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 127: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 127: Test timeout computed to be: 1500 123: .. 123: ---------------------------------------------------------------------- 123: Ran 2 tests in 0.018s 123: 123: OK 116/223 Test #123: pyTestMHFP ............................. Passed 0.40 sec test 128 Start 128: testMMFFForceFieldHelpers 128: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 128: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 128: Test timeout computed to be: 1500 128: [04:48:32] ------------------------------------- 128: [04:48:32] Test MMFF atom types. 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing MMFF builder tools. 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing MMFF builder+minimization. 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing Issue239. 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing calcEnergy with passed coords. 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing calcGrad. 122: ............. 122: ---------------------------------------------------------------------- 122: Ran 13 tests in 0.182s 122: 122: OK 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing Issue242. 111: =>start test GETAWAY 111: [04:48:32] test on : 365 molecules done 117/223 Test #111: testGETAWAY ............................ Passed 2.39 sec test 129 Start 129: testMMFFForceFieldHelpersMultiThread 129: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 129: Test timeout computed to be: 1500 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing github 308: crash during MMFF parameterization . 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing SFIssue1653802. 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Testing SFIssue2378119. 128: [04:48:32] done 128: [04:48:32] ------------------------------------- 128: [04:48:32] Test MMFF force-field parameter getters. 128: [04:48:32] ------------------------------------- 128: [04:48:32] Test MMFF multithreading 128: generating reference data 129: [04:48:32] ------------------------------------- 129: [04:48:32] Test MMFF multithreading 129: processing 129: launch :0 129: 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 :20 129: launch :21 129: launch :22 129: launch :23 64: [04:48:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [04:48:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [04:48:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [04:48:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 64: [04:48:32] deprecated group abbreviation ignored on line 24 64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] 64: [04:48:32] 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: 118/223 Test #122: pyTestGenerator ........................ Passed 0.83 sec test 130 Start 130: testUFFForceFieldHelpers 130: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 130: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 130: Test timeout computed to be: 1500 130: [04:48:32] ------------------------------------- 130: [04:48:32] Test UFF atom labels. 130: [04:48:32] done 130: [04:48:32] ------------------------------------- 130: [04:48:32] Test UFF atom typer. 130: [04:48:32] done 130: [04:48:32] ------------------------------------- 130: [04:48:32] Testing UFF builder tools. 130: [04:48:32] done 130: [04:48:32] ------------------------------------- 130: [04:48:32] Testing UFF builder+minimization. 127: ........ 127: ---------------------------------------------------------------------- 127: Ran 8 tests in 0.046s 127: 127: OK 125: ....... 125: ---------------------------------------------------------------------- 125: Ran 7 tests in 0.147s 125: 125: OK 130: [04:48:32] done 130: [04:48:32] ------------------------------------- 130: [04:48:32] Testing UFF special cases. 130: [04:48:32] UFFTYPER: Unrecognized charge state for atom: 0 130: [04:48:32] done 130: [04:48:32] ------------------------------------- 130: [04:48:32] Testing Issue239. 130: [04:48:32] done 130: [04:48:32] ------------------------------------- 130: [04:48:32] Testing calcEnergy with passed coords. 130: [04:48:32] done 130: [04:48:32] ------------------------------------- 130: [04:48:32] Testing calcGrad. 128: processing 128: launch :0 128: launch :1 128: launch :2 128: launch :3 130: [04:48:33] done 130: [04:48:33] ------------------------------------- 130: [04:48:33] Testing SFIssue1653802. 130: [04:48:33] done 130: [04:48:33] ------------------------------------- 130: [04:48:33] Testing SFIssue2378119. 130: [04:48:33] done 130: [04:48:33] ------------------------------------- 130: [04:48:33] Test UFF force-field parameter getters. 130: [04:48:33] ------------------------------------- 130: [04:48:33] Testing handling missing parameters. 130: [04:48:33] UFFTYPER: Unrecognized hybridization for atom: 0 130: [04:48:33] UFFTYPER: Unrecognized atom type: Cu+1 (0) 128: [04:48:33] Rep: 0 Mol:2 130: [04:48:33] UFFTYPER: Unrecognized hybridization for atom: 0 130: [04:48:33] UFFTYPER: Unrecognized atom type: Cu+1 (0) 128: [04:48:33] Rep: 0 Mol:0 130: [04:48:33] done 130: [04:48:33] ------------------------------------- 130: [04:48:33] Testing SFIssue3009337. 130: [04:48:33] done 130: [04:48:33] ------------------------------------- 130: [04:48:33] Test UFF multithreading 128: [04:48:33] Rep: 0 Mol:1 119/223 Test #127: pyMolTransforms ........................ Passed 0.69 sec test 131 Start 131: testCrystalForceField 131: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 131: Test timeout computed to be: 1500 128: [04:48:33] Rep: 0 Mol:5 128: [04:48:33] Rep: 0 Mol:3 128: [04:48:33] Rep: 0 Mol:9 128: [04:48:33] Rep: 0 Mol:13 128: [04:48:33] Rep: 0 Mol:4 128: [04:48:33] Rep: 0 Mol:17 128: [04:48:33] Rep: 0 Mol:6 130: generating reference data 128: [04:48:33] Rep: 0 Mol:10 131: ------------------------------------- 131: Test CrystalFF torsional term. 129: done 128: [04:48:33] Rep: 0 Mol:8 129: [04:48:33] done 128: [04:48:33] Rep: 0 Mol:12 128: [04:48:33] Rep: 0 Mol:16 128: [04:48:33] Rep: 0 Mol:7 128: [04:48:33] Rep: 0 Mol:21 128: [04:48:33] Rep: 0 Mol:11 128: [04:48:33] Rep: 0 Mol:15 128: [04:48:33] Rep: 0 Mol:25 128: [04:48:33] Rep: 0 Mol:19 128: [04:48:33] Rep: 0 Mol:20 128: [04:48:33] Rep: 0 Mol:23 128: [04:48:33] Rep: 0 Mol:27 128: [04:48:33] Rep: 0 Mol:31 128: [04:48:33] Rep: 0 Mol:29 120/223 Test #129: testMMFFForceFieldHelpersMultiThread ... Passed 0.53 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-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 132: Test timeout computed to be: 1500 128: [04:48:33] Rep: 0 Mol:14 128: [04:48:33] Rep: 0 Mol:24 128: [04:48:33] Rep: 0 Mol:18 128: [04:48:33] Rep: 0 Mol:28 128: [04:48:33] Rep: 0 Mol:22 121/223 Test #125: pyPartialCharges ....................... Passed 0.96 sec test 133 Start 133: testDistGeomHelpers 133: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 133: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 133: Test timeout computed to be: 1500 128: [04:48:33] Rep: 0 Mol:26 128: [04:48:33] Rep: 0 Mol:30 122/223 Test #131: testCrystalForceField .................. Passed 0.18 sec test 134 Start 134: distGeomHelpersCatch 134: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 134: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 134: Test timeout computed to be: 1500 133: go 133: ------------------------------------- 133: 134: Randomness seeded to: 2514370817 134: [04:48:33] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] 134: [04:48:33] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] 134: [04:48:33] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] 134: [04:48:33] [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: [04:48:33] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [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: ----------- 130: processing 130: launch :0 130: launch :1 130: launch :2 130: launch :3 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 134: ----------- 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 134: ----------- 130: [04:48:33] Rep: 0 Mol:1 130: [04:48:33] Rep: 0 Mol:5 130: [04:48:33] Rep: 0 Mol:9 130: [04:48:33] Rep: 0 Mol:0 130: [04:48:33] Rep: 0 Mol:3 134: ----------- 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] 134: [04:48:33] [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)] 130: [04:48:33] Rep: 0 Mol:4 130: [04:48:33] Rep: 0 Mol:2 130: [04:48:33] Rep: 0 Mol:13 130: [04:48:33] Rep: 0 Mol:8 130: [04:48:33] Rep: 0 Mol:7 130: [04:48:33] Rep: 0 Mol:17 130: [04:48:33] Rep: 0 Mol:11 130: [04:48:33] Rep: 0 Mol:15 130: [04:48:33] Rep: 0 Mol:19 130: [04:48:33] Rep: 0 Mol:12 130: [04:48:33] Rep: 0 Mol:16 128: [04:48:33] Rep: 20 Mol:3 128: [04:48:33] Rep: 20 Mol:7 128: [04:48:33] Rep: 20 Mol:11 128: [04:48:33] Rep: 20 Mol:15 128: [04:48:33] Rep: 20 Mol:19 128: [04:48:33] Rep: 20 Mol:23 128: [04:48:33] Rep: 20 Mol:27 128: [04:48:33] Rep: 20 Mol:31 130: [04:48:33] Rep: 0 Mol:23 130: [04:48:33] Rep: 0 Mol:27 130: [04:48:33] Rep: 0 Mol:31 130: [04:48:33] Rep: 0 Mol:6 130: [04:48:33] Rep: 0 Mol:10 130: [04:48:33] Rep: 0 Mol:20 130: [04:48:33] Rep: 0 Mol:24 130: [04:48:33] Rep: 0 Mol:21 130: [04:48:33] Rep: 0 Mol:28 130: [04:48:33] Rep: 0 Mol:25 130: [04:48:33] Rep: 0 Mol:29 130: [04:48:33] Rep: 0 Mol:14 130: [04:48:33] Rep: 0 Mol:18 128: [04:48:33] Rep: 20 Mol:1 128: [04:48:33] Rep: 20 Mol:5 128: [04:48:33] Rep: 20 Mol:9 128: [04:48:33] Rep: 20 Mol:13 128: [04:48:33] Rep: 20 Mol:17 128: [04:48:33] Rep: 20 Mol:21 128: [04:48:33] Rep: 20 Mol:25 128: [04:48:33] Rep: 20 Mol:29 134: [04:48:33] UFFTYPER: Unrecognized atom type: Pt5+2 (1) 134: [04:48:33] UFFTYPER: Unrecognized atom type: N_5 (2) 134: [04:48:33] UFFTYPER: Unrecognized atom type: N_5 (3) 134: [04:48:33] UFFTYPER: Unrecognized atom type: N_5 (2) 134: [04:48:33] UFFTYPER: Unrecognized atom type: N_5 (3) 128: [04:48:33] Rep: 20 Mol:2 128: [04:48:33] Rep: 20 Mol:6 128: [04:48:33] Rep: 20 Mol:10 128: [04:48:33] Rep: 20 Mol:14 128: [04:48:33] Rep: 20 Mol:18 130: [04:48:33] Rep: 0 Mol:22 130: [04:48:33] Rep: 0 Mol:26 128: [04:48:33] Rep: 20 Mol:22 128: [04:48:33] Rep: 20 Mol:26 128: [04:48:33] Rep: 20 Mol:30 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 1 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 1 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 1 130: [04:48:33] Rep: 0 Mol:30 128: [04:48:33] Rep: 20 Mol:0 128: [04:48:33] Rep: 20 Mol:4 128: [04:48:33] Rep: 20 Mol:8 128: [04:48:33] Rep: 20 Mol:12 128: [04:48:33] Rep: 20 Mol:16 128: [04:48:33] Rep: 20 Mol:20 128: [04:48:33] Rep: 20 Mol:24 128: [04:48:33] Rep: 20 Mol:28 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 5 128: [04:48:33] Rep: 40 Mol:3 128: [04:48:33] Rep: 40 Mol:7 128: [04:48:33] Rep: 40 Mol:11 128: [04:48:33] Rep: 40 Mol:15 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 5 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 5 128: [04:48:33] Rep: 40 Mol:19 128: [04:48:33] Rep: 40 Mol:23 128: [04:48:33] Rep: 40 Mol:27 128: [04:48:33] Rep: 40 Mol:31 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 6 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 6 134: [04:48:33] UFFTYPER: Unrecognized charge state for atom: 6 128: [04:48:33] Rep: 40 Mol:1 128: [04:48:33] Rep: 40 Mol:5 128: [04:48:33] Rep: 40 Mol:9 128: [04:48:33] Rep: 40 Mol:13 128: [04:48:33] Rep: 40 Mol:17 128: [04:48:33] Rep: 40 Mol:21 128: [04:48:33] Rep: 40 Mol:25 128: [04:48:33] Rep: 40 Mol:29 128: [04:48:33] Rep: 40 Mol:2 128: [04:48:33] Rep: 40 Mol:6 128: [04:48:33] Rep: 40 Mol:10 128: [04:48:33] Rep: 40 Mol:14 128: [04:48:33] Rep: 40 Mol:18 128: [04:48:33] Rep: 40 Mol:22 128: [04:48:33] Rep: 40 Mol:26 128: [04:48:33] Rep: 40 Mol:30 130: [04:48:33] Rep: 100 Mol:3 130: [04:48:33] Rep: 100 Mol:7 130: [04:48:33] Rep: 100 Mol:11 130: [04:48:33] Rep: 100 Mol:15 130: [04:48:33] Rep: 100 Mol:19 130: [04:48:33] Rep: 100 Mol:23 130: [04:48:33] Rep: 100 Mol:27 130: [04:48:33] Rep: 100 Mol:31 128: [04:48:33] Rep: 60 Mol:3 128: [04:48:33] Rep: 60 Mol:7 128: [04:48:33] Rep: 60 Mol:11 128: [04:48:33] Rep: 60 Mol:15 128: [04:48:33] Rep: 60 Mol:19 128: [04:48:33] Rep: 60 Mol:23 128: [04:48:33] Rep: 60 Mol:27 128: [04:48:33] Rep: 60 Mol:31 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: ..[04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 128: [04:48:33] Rep: 40 Mol:0 128: [04:48:33] Rep: 40 Mol:4 128: [04:48:33] Rep: 40 Mol:8 128: [04:48:33] Rep: 40 Mol:12 128: [04:48:33] Rep: 40 Mol:16 128: [04:48:33] Rep: 40 Mol:20 128: [04:48:33] Rep: 40 Mol:24 128: [04:48:33] Rep: 40 Mol:28 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 130: [04:48:33] Rep: 100 Mol:0 130: [04:48:33] Rep: 100 Mol:4 130: [04:48:33] Rep: 100 Mol:8 130: [04:48:33] Rep: 100 Mol:12 130: [04:48:33] Rep: 100 Mol:16 130: [04:48:33] Rep: 100 Mol:20 130: [04:48:33] Rep: 100 Mol:24 130: [04:48:33] Rep: 100 Mol:28 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 128: [04:48:33] Rep: 60 Mol:1 128: [04:48:33] Rep: 80 Mol:3 128: [04:48:33] Rep: 80 Mol:7 128: [04:48:33] Rep: 80 Mol:11 128: [04:48:33] Rep: 80 Mol:15 128: [04:48:33] Rep: 80 Mol:19 128: [04:48:33] Rep: 80 Mol:23 128: [04:48:33] Rep: 80 Mol:27 128: [04:48:33] Rep: 80 Mol:31 132: .[04:48:33] UFFTYPER: Unrecognized hybridization for atom: 0 132: [04:48:33] UFFTYPER: Unrecognized atom type: Cu+1 (0) 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[04:48:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: .[04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: ..[04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 132: [04:48:33] Molecule does not have explicit Hs. Consider calling AddHs() 128: [04:48:33] Rep: 60 Mol:5 128: [04:48:33] Rep: 60 Mol:9 128: [04:48:33] Rep: 60 Mol:13 128: [04:48:33] Rep: 60 Mol:17 128: [04:48:33] Rep: 60 Mol:21 128: [04:48:33] Rep: 60 Mol:2 128: [04:48:33] Rep: 60 Mol:6 128: [04:48:33] Rep: 60 Mol:10 128: [04:48:33] Rep: 60 Mol:25 128: [04:48:33] Rep: 60 Mol:29 128: [04:48:34] Rep: 60 Mol:14 128: [04:48:34] Rep: 60 Mol:18 128: [04:48:34] Rep: 60 Mol:22 128: [04:48:34] Rep: 60 Mol:26 128: [04:48:34] Rep: 60 Mol:30 132: [04:48:34] Molecule does not have explicit Hs. Consider calling AddHs() 130: [04:48:34] Rep: 100 Mol:1 130: [04:48:34] Rep: 100 Mol:5 130: [04:48:34] Rep: 100 Mol:9 130: [04:48:34] Rep: 100 Mol:13 130: [04:48:34] Rep: 100 Mol:17 130: [04:48:34] Rep: 100 Mol:21 130: [04:48:34] Rep: 100 Mol:25 130: [04:48:34] Rep: 100 Mol:29 132: ... 132: ---------------------------------------------------------------------- 132: Ran 18 tests in 0.289s 132: 132: OK 128: [04:48:34] Rep: 60 Mol:0 128: [04:48:34] Rep: 60 Mol:4 128: [04:48:34] Rep: 60 Mol:8 128: [04:48:34] Rep: 60 Mol:12 128: [04:48:34] Rep: 60 Mol:16 128: [04:48:34] Rep: 60 Mol:20 128: [04:48:34] Rep: 60 Mol:24 128: [04:48:34] Rep: 60 Mol:28 128: [04:48:34] Rep: 80 Mol:1 128: [04:48:34] Rep: 80 Mol:5 128: [04:48:34] Rep: 80 Mol:9 128: [04:48:34] Rep: 80 Mol:13 128: [04:48:34] Rep: 80 Mol:17 128: [04:48:34] Rep: 80 Mol:21 128: [04:48:34] Rep: 80 Mol:25 128: [04:48:34] Rep: 80 Mol:29 123/223 Test #132: pyForceFieldHelpers .................... Passed 1.16 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-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 135: Test timeout computed to be: 1500 128: [04:48:34] Rep: 80 Mol:2 128: [04:48:34] Rep: 80 Mol:6 128: [04:48:34] Rep: 80 Mol:10 128: [04:48:34] Rep: 80 Mol:14 128: [04:48:34] Rep: 80 Mol:18 128: [04:48:34] Rep: 80 Mol:22 128: [04:48:34] Rep: 80 Mol:26 128: [04:48:34] Rep: 80 Mol:30 106: =>start test GETAWAY custom 106: [04:48:34] test on : 365 molecules done 124/223 Test #106: testRDFcustom .......................... Passed 5.30 sec test 136 Start 136: testMolAlign 136: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 136: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 136: Test timeout computed to be: 1500 130: [04:48:34] Rep: 100 Mol:2 130: [04:48:34] Rep: 100 Mol:6 130: [04:48:34] Rep: 100 Mol:10 130: [04:48:34] Rep: 100 Mol:14 130: [04:48:34] Rep: 100 Mol:18 130: [04:48:34] Rep: 100 Mol:22 130: [04:48:34] Rep: 100 Mol:26 130: [04:48:34] Rep: 100 Mol:30 128: [04:48:34] Rep: 80 Mol:0 128: [04:48:34] Rep: 80 Mol:4 128: [04:48:34] Rep: 80 Mol:8 128: [04:48:34] Rep: 80 Mol:12 128: [04:48:34] Rep: 80 Mol:16 128: [04:48:34] Rep: 80 Mol:20 128: [04:48:34] Rep: 80 Mol:24 128: [04:48:34] Rep: 80 Mol:28 136: *********************************************************** 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: *********************************************************** 125/223 Test #136: testMolAlign ........................... Passed 0.25 sec test 137 Start 137: testO3AAlign 137: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 137: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 137: Test timeout computed to be: 1500 128: [04:48:34] done 128: [04:48:34] ------------------------------------- 128: [04:48:34] Test MMFF multithreading2 134: [04:48:35] UFFTYPER: Warning: hybridization set to SP3 for atom 6 135: .[04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: ..[04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: ..[04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: .[04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 130: [04:48:35] done 130: [04:48:35] ------------------------------------- 130: [04:48:35] Test UFF multithreading2 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 134: [04:48:35] UFFTYPER: Warning: hybridization set to SP3 for atom 6 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 134: [04:48:35] UFFTYPER: Warning: hybridization set to SP3 for atom 6 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 134: [04:48:35] UFFTYPER: Warning: hybridization set to SP3 for atom 11 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 128: [04:48:35] done 128: [04:48:35] ------------------------------------- 128: [04:48:35] Test MMFF multithreading3 134: [04:48:35] UFFTYPER: Warning: hybridization set to SP3 for atom 11 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 134: [04:48:35] UFFTYPER: Warning: hybridization set to SP3 for atom 11 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:48:35] Molecule does not have explicit Hs. Consider calling AddHs() 135: .[04:48:36] Molecule does not have explicit Hs. Consider calling AddHs() 26: All 191 tests passed 130: [04:48:36] done 130: [04:48:36] ------------------------------------- 130: [04:48:36] Test UFF multithreading3 26: 26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 135: [04:48:36] Molecule does not have explicit Hs. Consider calling AddHs() 128: [04:48:36] done 128: [04:48:36] ------------------------------------- 128: [04:48:36] Testing github 162: Incorrect SMILES after MMFF parameterization . 128: [04:48:36] done 128: [04:48:36] ------------------------------------- 128: [04:48:36] Testing github 224: crash during MMFF parameterization . 128: [04:48:36] done 128: [04:48:36] ------------------------------------- 128: [04:48:36] Testing github6728: crash due to missing stretch-bend params. 126/223 Test #128: testMMFFForceFieldHelpers .............. Passed 3.90 sec test 138 Start 138: molAlignCatchTest 138: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 138: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 138: Test timeout computed to be: 1500 135: [04:48:36] Molecule does not have explicit Hs. Consider calling AddHs() 138: Randomness seeded to: 3871851897 138: 170567759 138: 141515836 135: [04:48:36] Molecule does not have explicit Hs. Consider calling AddHs() 130: [04:48:36] done 130: [04:48:36] ------------------------------------- 130: [04:48:36] Testing GitHubIssue62. 130: [04:48:36] beta-lactam 39.6387 130: [04:48:36] cyclopropanone 174.698 130: [04:48:36] aziridine 337.986 130: [04:48:36] aziridinone 115.248 130: [04:48:36] isobutene 2.48217 130: [04:48:36] acetone 1.91788 130: [04:48:36] cyclopentanone 10.1648 130: [04:48:36] cyclopropene 99.4921 130: [04:48:36] cyclobutene 41.0156 130: [04:48:36] cyclopropane 267.236 130: [04:48:36] gamma-lactam 15.7471 130: [04:48:36] trans-2,3-diphenylcyclopropan-1-one 203.398 130: [04:48:36] cis-2,3-diphenylcyclopropan-1-one 206.852 133: building molecules 130: [04:48:36] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 130: [04:48:36] cyclopropylidencyclobutane 218.879 133: generating reference data 130: [04:48:37] diphenylmethylidencyclobutane 79.6139 130: [04:48:37] done 130: [04:48:37] ------------------------------------- 130: [04:48:37] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. 130: [04:48:37] done 130: [04:48:37] ------------------------------------- 130: [04:48:37] Test square planar complexes 130: [04:48:37] done 130: [04:48:37] ------------------------------------- 130: [04:48:37] Test octahedral complexes 130: [04:48:37] done 127/223 Test #130: testUFFForceFieldHelpers ............... Passed 4.25 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-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap 139: Test timeout computed to be: 1500 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Test GitHub Issue 258: Bad pattern fingerprint for query molecule 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Test unfolded version of RDKFP 117: [04:48:37] ------------------------------------- 117: [04:48:37] Test bitinfo of RDKFP 117: 562: [ 2 ], 117: 709: [ 0 1 ], 117: 1118: [ 0 1 2 ], 117: 1183: [ 1 2 ], 117: 1233: [ 0 1 2 ], 117: 1308: [ 0 ], [ 1 ], 117: 1339: [ 2 ], 117: 1728: [ 1 2 ], 117: 1772: [ 0 ], [ 1 ], 117: 1813: [ 0 1 ], 117: ------------ 117: [04:48:37] ------------------------------------- 117: [04:48:37] Single atoms setting radius 1 bits in Morgan fingerprints 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Github #879: Pattern fingerprint should set bits for single-atom fragments. 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Github #2115: BitInfo not complete for RDKFingerprint 117: [04:48:37] done 117: [04:48:37] ------------------------------------- 117: [04:48:37] Github #3723: Fingerprint crash for mols with Zero order bonds 117: [04:48:37] done 128/223 Test #117: testFingerprints ....................... Passed 6.20 sec test 140 Start 140: testFeatures 140: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 140: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 140: Test timeout computed to be: 1500 140: [04:48:37] ------------------------------------- 140: [04:48:37] AtomType parser testing. 140: [04:48:37] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] 140: [04:48:37] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] FeatureDefinition parser testing. 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Test pulling feat defs from a string. 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] FeatureDef functionality testing. 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] FeatureFactory testing. 140: [04:48:37] 1 140: [04:48:37] 2 140: [04:48:37] 3 140: [04:48:37] 4 140: [04:48:37] 5 140: [04:48:37] 6 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Feature Location testing. 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Test building a FeatureFactory from a file 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Testing Issue 224. 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Testing Issue 225. 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Test Issue346 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Test Issue347 140: [04:48:37] done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Testing Issue 348. 140: [04:48:37] SMARTS Parse Error: syntax error while parsing: [C[C] 140: [04:48:37] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' 140: [04:48:37] ------------------------------------- 140: [04:48:37] Testing Nested AtomType definitions. 140: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] 140: [04:48:37] ------------------------------------- 140: [04:48:37] Testing Github Issue #252: crash when calling getPos() with no conformer. 140: [04:48:37] expect a precondition failure message below 140: [04:48:37] 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: [04:48:37] Done 140: [04:48:37] ------------------------------------- 140: [04:48:37] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() 140: [04:48:37] done 129/223 Test #140: testFeatures ........................... Passed 0.04 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-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 141: Test timeout computed to be: 1500 135: [04:48:37] Molecule does not have explicit Hs. Consider calling AddHs() 64: [04:48:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 64: [04:48:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 64: ---------------------------------- 64: ---------------------------------- 64: [04:48:37] 64: 64: **** 64: Pre-condition Violation 64: rlabel out of range for MDL files 64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp 64: Failed Expression: rlabel >= 0 && rlabel < 100 64: **** 64: 64: [04:48:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 135: [04:48:37] Molecule does not have explicit Hs. Consider calling AddHs() 64: [04:48:37] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas 64: [04:48:37] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 64: [04:48:37] Empty atom list: 'M ALS 1 0 F' on line 8. 130/223 Test #64: fileParsersTest1 ....................... Passed 12.57 sec test 142 Start 142: testShapeHelpers 142: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 142: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers 142: Test timeout computed to be: 1500 142: *********************************************************** 142: Testing ShapeHelpers 142: --------------------------------- 142: test1Encode 142: 142: --------------------------------- 142: test2Compare 142: 142: --------------------------------- 142: testGithub4364 142: 142: *********************************************************** 131/223 Test #142: testShapeHelpers ....................... Passed 0.05 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-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 143: Test timeout computed to be: 1500 141: .[04:48:37] Molecule does not have explicit Hs. Consider calling AddHs() 141: .[04:48:37] Molecule does not have explicit Hs. Consider calling AddHs() 141: ..[04:48:37] Molecule does not have explicit Hs. Consider calling AddHs() 141: .[04:48:37] Molecule does not have explicit Hs. Consider calling AddHs() 141: .[04:48:37] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] 141: [04:48:37] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 141: ... 141: ---------------------------------------------------------------------- 141: Ran 9 tests in 0.095s 141: 141: OK 132/223 Test #141: pyChemicalFeatures ..................... Passed 0.67 sec test 144 Start 144: testMolCatalog 144: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 144: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 144: Test timeout computed to be: 1500 133/223 Test #144: testMolCatalog ......................... Passed 0.03 sec test 145 Start 145: pyMolCatalog 145: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 145: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 145: Test timeout computed to be: 1500 84: 0,0 0 84: 0,1 0 84: 1,0 0 84: 1,1 0 84: 2,0 0 84: 2,1 0 134/223 Test #84: testEnumeration ........................ Passed 11.62 sec test 146 Start 146: moldraw2DTest1 146: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 146: Test timeout computed to be: 1500 146: ----------------- Test 1 143: . 143: ---------------------------------------------------------------------- 143: Ran 1 test in 0.055s 143: 143: OK 143: Testing Shape Helpers wrapper 146: file test1_6.svg gave hash 1109656969U not the expected 2635907956U 146: Done 146: ----------------- Test 2 146: file test2_1.png gave hash 3662870653U not the expected 307437906U 146: file test2_2.png gave hash 3839236620U not the expected 610424244U 146: file test2_3.png gave hash 2294574389U not the expected 2179746375U 146: Done 146: ----------------- Test 4 146: file test4_1.png gave hash 1974149556U not the expected 1403972924U 146: Done 146: ----------------- Test 5 146: file test5_1.png gave hash 2006087519U not the expected 1269428339U 146: file test5_2.png gave hash 3967299996U not the expected 3073694291U 146: file test5_3.png gave hash 2767610192U not the expected 1865192682U 146: Done 146: ----------------- Test 6 (atom labels) 146: Done 146: ----------------- Test 7 (backgrounds) 135/223 Test #143: pyShapeHelpers ......................... Passed 0.61 sec test 147 Start 147: moldraw2DTestCatch 147: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 147: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 147: Test timeout computed to be: 1500 146: file test7_1.png gave hash 4080154814U not the expected 3033050306U 146: file test7_2.png gave hash 366251741U not the expected 3476380724U 146: Done 146: ----------------- Test8: PrepareMolDrawing 146: Done 146: ----------------- Test multi-threaded drawing 146: reading molecules 146: generating reference drawings 147: Randomness seeded to: 2370749732 147: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U 147: file contourMol_2.svg gave hash 2850811663U not the expected 572669511U 146: processing 146: launch :0 146: launch :1 146: launch :2 146: launch :3 147: file contourMol_3.svg gave hash 1894450507U not the expected 936771429U 147: file contourMol_4.svg gave hash 4223940354U not the expected 3302971362U 147: file contourMol_5.svg gave hash 1093404576U not the expected 2230414999U 147: file testGithub3226_1.png gave hash 1298537421U not the expected 2350054896U 147: file testGithub3226_2.png gave hash 4249073986U not the expected 606206725U 147: file testGithub3226_3.png gave hash 1401608198U not the expected 2282880418U 147: file testPNGMetadata_1.png gave hash 2404275697U not the expected 2423299691U 145: . 145: ---------------------------------------------------------------------- 145: Ran 1 test in 0.014s 145: 145: OK 147: file testPNGMetadata_2.png gave hash 2335719695U not the expected 2803353117U 147: file testGithub3369_1.svg gave hash 1012801087U not the expected 3091976328U 147: [04:48:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 138: 1815660729 147: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U 147: [04:48:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-1.png gave hash 3017698331U not the expected 698316547U 147: [04:48:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-2.svg gave hash 1182231268U not the expected 4132716144U 147: [04:48:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 136/223 Test #145: pyMolCatalog ........................... Passed 0.84 sec test 148 Start 148: moldraw2DRxnTest1 148: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 148: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 148: Test timeout computed to be: 1500 147: file testHandDrawn-2.png gave hash 1476321984U not the expected 1605553248U 147: [04:48:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:38] 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: [04:48:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-3.png gave hash 3459141761U not the expected 2881952238U 147: [04:48:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:38] 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: [04:48:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-4.png gave hash 751103982U not the expected 3431655453U 148: ----------------- Test 1 148: file rxn_test1_1.png gave hash 3931149906U not the expected 1556334749U 148: file rxn_test1_2.png gave hash 665316462U not the expected 1924084263U 148: file rxn_test1_3.png gave hash 583399715U not the expected 1644921059U 148: file rxn_test1_4.png gave hash 3197024324U not the expected 2471435686U 148: file rxn_test1_5.png gave hash 3779444276U not the expected 1428782307U 148: file rxn_test1_6.png gave hash 4083260446U not the expected 483353696U 135: [04:48:38] Molecule does not have explicit Hs. Consider calling AddHs() 148: file rxn_test1_7.png gave hash 3485241449U not the expected 528963379U 148: Done 148: ----------------- Test 2: some examples that caused problems in testing 148: file rxn_test2_1.png gave hash 4000022879U not the expected 399415052U 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 148: file rxn_test2_2_1.png gave hash 1840548677U not the expected 1215378243U 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 148: file rxn_test2_2_2.png gave hash 751090601U not the expected 3645141778U 148: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 148: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 148: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C 148: file rxn_test2_2_3.png gave hash 4146401115U not the expected 551946805U 148: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC 148: file rxn_test2_2_4.png gave hash 3607216253U not the expected 4234617566U 148: Done 148: ----------------- Test 3: test reactant highlighting 148: file rxn_test3_1.png gave hash 663098801U not the expected 4176857511U 148: file rxn_test3_1.svg gave hash 2319756417U not the expected 2165658826U 148: Done 148: ----------------- Test 4: some examples from SMARTS in testing 148: draw! 148: file rxn_test4_1.png gave hash 2172852570U not the expected 4187207676U 148: file rxn_test4_1.svg gave hash 2304233907U not the expected 3239755313U 148: done 135: [04:48:39] Molecule does not have explicit Hs. Consider calling AddHs() 148: file rxn_test4_2.png gave hash 3573150360U not the expected 3490081297U 148: file rxn_test4_2.svg gave hash 4061413684U not the expected 4127054729U 148: Done 137/223 Test #148: moldraw2DRxnTest1 ...................... Passed 0.52 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-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 149: Test timeout computed to be: 1500 138: 601513382 138: =============================================================================== 138: All tests passed (73 assertions in 3 test cases) 138: 138/223 Test #138: molAlignCatchTest ...................... Passed 2.99 sec test 150 Start 150: testFMCS 150: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS 150: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS 150: Test timeout computed to be: 1500 135: [04:48:39] Molecule does not have explicit Hs. Consider calling AddHs() 147: file testHandDrawn-5a.svg gave hash 2478133241U not the expected 3628607349U 147: [04:48:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-5b.svg gave hash 2108082312U not the expected 2522138089U 147: [04:48:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. 147: [04:48:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-5.png gave hash 205144647U not the expected 3439548169U 147: file testBrackets-5a.svg gave hash 4023768529U not the expected 3061667963U 147: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 147: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 147: file testPositionVariation-1b.svg gave hash 823876785U not the expected 174339626U 149: ...[04:48:39] Font file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. 149: [04:48:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 149: ..........[04:48:39] 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: 147: [04:48:39] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U 135: [04:48:39] Molecule does not have explicit Hs. Consider calling AddHs() 147: file testGithub4238_1.png gave hash 697827931U not the expected 3410617836U 147: file testGithub4323_1.png gave hash 1827938735U not the expected 3723958844U 133: validating reference data 149: ..................... 149: ---------------------------------------------------------------------- 149: Ran 34 tests in 0.261s 149: 149: OK 149: json lasso 147: file testGithub4323_3.png gave hash 119218767U not the expected 2185913679U 147: [04:48:40] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 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 139/223 Test #149: pyMolDraw2D ............................ Passed 0.94 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-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap 151: Test timeout computed to be: 1500 135: [04:48:40] Molecule does not have explicit Hs. Consider calling AddHs() 26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 147: file testFlexiCanvas.2a.png gave hash 4234574492U not the expected 3217758043U 147: file testFlexiCanvas.2b.png gave hash 615048826U not the expected 4070063910U 147: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U 147: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U 147: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U 147: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U 147: file testGithub4764.sz1.png gave hash 4114540222U not the expected 98827714U 147: file testGithub4764.sz2.png gave hash 868193289U not the expected 89252465U 147: file testGithub4764.sz3.png gave hash 2835449234U not the expected 148503574U 147: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U 147: file github5383_1.svg gave hash 2850811663U not the expected 3666750661U 147: file github5383_2.svg gave hash 1346330069U not the expected 0U 147: file github5383_1.png gave hash 3310569434U not the expected 992803933U 147: file acs1996_1.png gave hash 1909632721U not the expected 2957839025U 147: file acs1996_2.png gave hash 1539606209U not the expected 2664798808U 147: file acs1996_3.svg gave hash 510450189U not the expected 879041204U 147: file acs1996_8.svg gave hash 10362698U not the expected 2477908768U 147: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U 147: [04:48:40] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. 147: file bond_highlights_8.svg gave hash 1272407071U not the expected 2956924065U 26: All 191 tests passed 26: done 26: ------------------------------------- 26: Unit tests for all MMFF constraint terms. 147: file test_github5947.svg gave hash 4282730978U not the expected 337972125U 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. 147: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U 26: done 26: ------------------------------------- 26: Unit test for MMFF butane scan. 147: file github6336_1.png gave hash 1930712448U not the expected 2958833204U 147: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U 147: file github6504_2.svg gave hash 106020287U not the expected 2871662880U 147: file github6569_1.svg gave hash 1698514747U not the expected 116573839U 147: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U 147: =============================================================================== 147: All tests passed (6525 assertions in 94 test cases) 147: 140/223 Test #147: moldraw2DTestCatch ..................... Passed 2.46 sec test 152 Start 152: FMCStest 152: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 152: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test 152: Test timeout computed to be: 1500 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): 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 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): 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 26: done 135: [04:48:40] Molecule does not have explicit Hs. Consider calling AddHs() 141/223 Test #26: testMMFFForceField ..................... Passed 17.27 sec 142/223 Test #152: FMCStest ............................... Passed 0.09 sec test 153 Start 153: molHashCatchTest 153: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 153: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 153: Test timeout computed to be: 1500 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-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 154: Test timeout computed to be: 1500 153: Randomness seeded to: 720370166 153: =============================================================================== 153: All tests passed (304 assertions in 9 test cases) 153: 143/223 Test #153: molHashCatchTest ....................... Passed 0.07 sec test 155 Start 155: testMMPA 155: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/testMMPA 155: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA 155: Test timeout computed to be: 1500 155: 155: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 155: Time elapsed 0.001814 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. 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. 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. 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. 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. 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 0.001602 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 = 12 155: 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 = 3 155: 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 = 2 155: 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 0.001603 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 = 6 155: 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. 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 = 2 155: 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 0.000457 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 = 3 155: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 155: 3: NOREF. Reference data NOT LISTED in test case. 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 = 5 155: 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 = 7 155: 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 0.001790 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. 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. 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. 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. 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. 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 0.001811 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. 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. 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. 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. 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. 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. 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. 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. 155: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 155: 18: NOREF. Reference data NOT LISTED in test case. 155: 155: --- ALL PASSED --- 155: ----------------------------------- 155: 5 TEST CASES FAILED 144/223 Test #155: testMMPA ............................... Passed 0.06 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-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap 156: Test timeout computed to be: 1500 154: ... 154: ---------------------------------------------------------------------- 154: Ran 3 tests in 0.011s 154: 154: OK 145/223 Test #154: pyMolHash .............................. Passed 0.50 sec test 157 Start 157: testRascalMCES 157: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 157: Test timeout computed to be: 1500 137: processing 137: launch :0 137: launch :1 137: launch :2 137: launch :3 135: .[04:48:41] Molecule does not have explicit Hs. Consider calling AddHs() 150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 150: Time elapsed 0.008 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 0.116 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 0.025 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 0.024 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 0.195 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 0.170 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 0.207 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 0.207 seconds 150: 150: testSegFault() 150: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 150: Time elapsed 0.013 seconds 150: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds 150: Time elapsed 0.023 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 0.019 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 0.575 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 0.585 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 0.651 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 0.013 seconds 150: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds 150: Time elapsed 0.013 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 0.012 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 0.162 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 0.051 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 0.0009 seconds. bond[0]=6 150: STATISTICS: 150: Total Growing Steps = 1, MCS found on 1 step, for 0.0009 seconds 150: Initial Seeds = 1, Mismatched 0 150: Inspected Seeds = 2 150: Rejected by BestSize = 0 150: IndividualBondExcluded = 0 150: MatchCheck Seeds = 2 150: MatchCalls = 2 150: MatchFound = 1 150: fastMatchCalls = 1 150: fastMatchFound = 0 150: slowMatchCalls = 2 150: slowMatchFound = 1 150: DupCacheFound = 0 0 matched, 0 mismatched 150: HashCache size = 1 keys 150: HashCache size = 1 entries 150: FindHashInCache = 2 150: HashFoundInCache= 0 150: ExactMatchCalls = 0 150: ExactMatchFound = 0 150: Time elapsed 0.001 seconds 150: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 150: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 150: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 150: res sub = 1 size=3 150: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 150: res sub = 1 size=3 150: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds 150: test target = CC[C@H](F)Cl query = CCC useChirality = 0 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = CC[C@H](F)Cl query = CCC useChirality = 1 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = CCC(F)Cl query = CC useChirality = 0 150: res sub = 1 size=2 150: MCS: [#6]-[#6] 2 atoms, 1 bonds 150: test target = CCC(F)Cl query = CC useChirality = 1 150: res sub = 1 size=2 150: MCS: [#6]-[#6] 2 atoms, 1 bonds 150: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 150: res sub = 0 size=0 150: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 150: res sub = 0 size=0 150: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 150: res sub = 0 size=0 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = OC(F)CCl query = OC(F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = OC(F)CCl query = OC(F)C useChirality = 1 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 150: res sub = 0 size=0 150: MCS: [#9] 1 atoms, 0 bonds 150: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 150: res sub = 1 size=4 150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 150: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 150: res sub = 0 size=0 150: MCS: [#9] 1 atoms, 0 bonds 150: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 150: res sub = 1 size=3 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 150: res sub = 1 size=3 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 150: res sub = 1 size=3 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 150: res sub = 1 size=3 150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 150: 150: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> 150: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: done 133: processing 133: launch :0 133: launch :1 133: launch :2 133: launch :3 156: ......... 156: ---------------------------------------------------------------------- 156: Ran 9 tests in 1.811s 156: 156: OK 146/223 Test #156: pyMMPA ................................. Passed 2.52 sec test 158 Start 158: testRascalCluster 158: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 158: Test timeout computed to be: 1500 150: [04:48:44] The provided InitialSeed is not an MCS and will be ignored 151: ........................................[04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: [04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: [04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: .[04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: [04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: [04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: .[04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: [04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: [04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: .[04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: [04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: [04:48:45] The provided InitialSeed is not an MCS and will be ignored 151: ................. 151: ---------------------------------------------------------------------- 151: Ran 60 tests in 4.505s 151: 151: OK 147/223 Test #151: pyFMCS ................................. Passed 5.33 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-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 159: Test timeout computed to be: 1500 135: ..[04:48:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 146: Done 146: ----------------- Test Github #781: Rendering single-atom molecules 146: Done 146: ----------------- Test 3 146: file test3_1.png gave hash 3995200969U not the expected 3984824963U 146: file test3_2.png gave hash 1726535510U not the expected 238321316U 146: file test3_3.png gave hash 1289881546U not the expected 414888185U 146: file test3_3.svg gave hash 1119144208U not the expected 1375178959U 146: file test3_4.png gave hash 3140382753U not the expected 2265825690U 146: file test3_4.svg gave hash 2680534430U not the expected 187720898U 146: file test3_5.png gave hash 3099888250U not the expected 1911551403U 159: ........ 159: ---------------------------------------------------------------------- 159: Ran 8 tests in 1.837s 159: 159: OK 146: file test3_5.svg gave hash 2157820698U not the expected 2015616393U 146: file test3_6.png gave hash 2620932115U not the expected 577293879U 146: file test3_7.png gave hash 807230453U not the expected 248355372U 146: Done 146: ----------------- Test Github774: upside-down drawings 146: file test774_1.png gave hash 3121030024U not the expected 927423591U 146: file test774_2.png gave hash 2368659339U 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 146: file test852_1.png gave hash 2345477955U not the expected 736085072U 148/223 Test #159: pyMolDraw2D ............................ Passed 2.44 sec test 160 Start 160: testCIPLabeler 160: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 160: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler 160: Test timeout computed to be: 1500 146: file test852_2.png gave hash 2980031162U 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 988661147U not the expected 2065140854U 160: Randomness seeded to: 1075593297 160: [04:48:48] non kekulizable aromatic bond being treated as bond order 1 160: [04:48:48] non kekulizable aromatic bond being treated as bond order 1 160: [04:48:48] non kekulizable aromatic bond being treated as bond order 1 160: [04:48:48] non kekulizable aromatic bond being treated as bond order 1 160: [04:48:48] non kekulizable aromatic bond being treated as bond order 1 160: [04:48:48] non kekulizable aromatic bond being treated as bond order 1 146: file test860_2.png gave hash 1783539966U not the expected 3098360765U 146: file test860_3.png gave hash 55970806U 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 160: =============================================================================== 160: All tests passed (5977 assertions in 13 test cases) 160: 146: Done 146: ----------------- Testing drawMolecules 149/223 Test #160: testCIPLabeler ......................... Passed 0.20 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-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 161: Test timeout computed to be: 1500 146: file test12_1.svg gave hash 2982175789U not the expected 881731720U 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. 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 255849476U not the expected 4119581143U 146: file testGithub2151_2.svg gave hash 1195866900U 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 608211058U not the expected 3635831631U 146: file testGithub2931_3.svg gave hash 1702246706U not the expected 2885834646U 146: Done 146: ----------------- Testing annotation of 2D Drawing. 146: file test20_1.png gave hash 3948107650U not the expected 1672353490U 146: file test20_2.png gave hash 2454497089U not the expected 1073213605U 146: file test20_3.png gave hash 2576848427U not the expected 471234756U 146: file test20_4.png gave hash 2436713093U 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 3566226990U not the expected 1801411420U 161: ... 161: ---------------------------------------------------------------------- 161: Ran 3 tests in 0.014s 161: 161: OK 146: file testGithub3305_2.png gave hash 3262469175U not the expected 2904846519U 146: file testGithub3305_3.png gave hash 2042445738U not the expected 2915229647U 146: file testGithub3305_4.png gave hash 3099888250U not the expected 1911551403U 146: file testGithub3305_4.svg gave hash 2157820698U not the expected 2015616393U 146: file testGithub3305_5.png gave hash 1702931839U not the expected 614319597U 146: file testGithub3305_5.svg gave hash 911738919U not the expected 3435115096U 150/223 Test #161: pyCIPLabelsWrapTest .................... Passed 0.72 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-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 162: Test timeout computed to be: 1500 146: file testGithub3305_6.png gave hash 4041722001U not the expected 3926947401U 146: file testGithub3305_7.png gave hash 1767819280U 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 151/223 Test #146: moldraw2DTest1 ......................... Passed 10.94 sec test 163 Start 163: deprotectTest 163: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 163: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect 163: Test timeout computed to be: 1500 163: Randomness seeded to: 113641273 163: =============================================================================== 163: All tests passed (111 assertions in 3 test cases) 163: 152/223 Test #163: deprotectTest .......................... Passed 0.15 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-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap 164: Test timeout computed to be: 1500 164: ..... 164: ---------------------------------------------------------------------- 164: Ran 5 tests in 0.074s 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 153/223 Test #164: pyDeprotect ............................ Passed 0.95 sec test 165 Start 165: testReducedGraphs 165: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 165: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs 165: 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, 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, 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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: 154/223 Test #165: testReducedGraphs ...................... Passed 0.09 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-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 166: Test timeout computed to be: 1500 158: Randomness seeded to: 888847131 158: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi 166: ..... 166: ---------------------------------------------------------------------- 166: Ran 5 tests in 0.029s 166: 166: OK 155/223 Test #166: pyReducedGraphs ........................ Passed 0.81 sec test 167 Start 167: trajectoryTest 167: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 167: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory 167: Test timeout computed to be: 1500 156/223 Test #167: trajectoryTest ......................... Passed 0.63 sec test 168 Start 168: substructLibraryTest 168: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 168: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 168: Test timeout computed to be: 1500 168: [04:48:51] ------------------------------------- 168: [04:48:51] Test1 168: [04:48:52] done 168: [04:48:52] ------------------------------------- 168: [04:48:52] Test2 157: Randomness seeded to: 2458832592 157: Timed out after 11 seconds. 168: [04:48:52] done 168: [04:48:52] ------------------------------------- 168: [04:48:52] Test3 (stereo options) 168: [04:48:52] Done (stereo options) 168: [04:48:52] ------------------------------------- 168: [04:48:52] Test4 (trusted smiles) 168: [04:48:52] Done (trusted smiles) 168: [04:48:52] ------------------------------------- 168: [04:48:52] Testing C++ docs 168: [04:48:52] Done (C++ doc tests) 168: [04:48:52] ------------------------------------- 168: [04:48:52] Testing C++ ring query: PatternHolder 168: [04:48:52] Done (C++ ring query tests) 168: [04:48:52] ------------------------------------- 168: [04:48:52] Testing C++ ring query: TautomerPatternHolder 168: [04:48:52] Done (C++ ring query tests) 168: [04:48:52] ------------------------------------- 168: [04:48:52] Add Patterns 139: .............[04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:54] Molecule does not have explicit Hs. Consider calling AddHs() 168: [04:48:59] ------------------------------------- 168: [04:48:59] testing PatternHolder 139: ...[04:48:59] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:59] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:59] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:59] Molecule does not have explicit Hs. Consider calling AddHs() 139: [04:48:59] Molecule does not have explicit Hs. Consider calling AddHs() 139: ... 139: ---------------------------------------------------------------------- 139: Ran 19 tests in 22.109s 139: 139: OK 139: Testing MolAlign Wrappers 168: [04:48:59] ------------------------------------- 168: [04:48:59] testing TautomerPatternHolder 157/223 Test #139: pyMolAlign ............................. Passed 22.64 sec test 169 Start 169: substructLibraryCatchTest 169: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 169: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 169: Test timeout computed to be: 1500 168: [04:48:59] ------------------------------------- 168: [04:48:59] testSegFaultInHolder 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: [04:48:59] syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] SMILES Parse Error: syntax error while parsing: dsafsdf 168: [04:48:59] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 168: [04:48:59] ------------------------------------- 168: [04:48:59] Results do not depend on numThreads 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: 158/223 Test #162: pyCIPLabelsValidation .................. Passed 12.07 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-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 170: Test timeout computed to be: 1500 169: Randomness seeded to: 2985333334 169: =============================================================================== 169: All tests passed (171 assertions in 5 test cases) 169: 159/223 Test #169: substructLibraryCatchTest .............. Passed 1.88 sec test 171 Start 171: testRGroupDecomp 171: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 171: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 171: Test timeout computed to be: 1500 171: [04:49:02] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters 171: [04:49:02] WARNING: not removing hydrogen atom with dummy atom neighbors 137: --------------------------------- 137: test O3A multithreading bug 137: 137: --------------------------------- 137: testCrippenO3A multithreading 137: 137: generating reference data 137: processing 137: launch :0 137: launch :1 137: launch :2 137: launch :3 168: [04:49:04] ------------------------------------- 168: [04:49:04] Results do not depend on numThreads (all same) 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 25.15 seconds 160/223 Test #150: testFMCS ............................... Passed 25.23 sec test 172 Start 172: testRGroupDecompInternals 172: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 172: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 172: Test timeout computed to be: 1500 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 172: [04:49:04] WARNING: not removing hydrogen atom with dummy atom neighbors 161/223 Test #172: testRGroupDecompInternals .............. Passed 0.06 sec test 173 Start 173: rgroupCatchTests 173: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 173: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 173: Test timeout computed to be: 1500 168: [04:49:04] ------------------------------------- 168: [04:49:04] testTautomerQueries 168: [04:49:04] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... 168: [04:49:04] ------------------------------------- 168: [04:49:04] github3881 recursive smarts with rings 162/223 Test #168: substructLibraryTest ................... Passed 13.29 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-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 174: Test timeout computed to be: 1500 173: Randomness seeded to: 4156905523 173: =============================================================================== 173: All tests passed (203 assertions in 13 test cases) 173: 163/223 Test #173: rgroupCatchTests ....................... Passed 0.32 sec test 175 Start 175: molInterchangeTest1 175: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 175: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 175: Test timeout computed to be: 1500 175: [04:49:05] test1: basics 175: [04:49:05] done 175: [04:49:05] 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: [04:49:05] done 175: [04:49:05] 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: [04:49:05] done 175: [04:49:05] 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: [04:49:05] done 175: [04:49:05] 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: [04:49:05] testing parse options 175: [04:49:05] done 175: [04:49:05] 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: [04:49:05] done 175: [04:49:05] testing 'either' stereochemistry 175: [04:49:05] done 164/223 Test #175: molInterchangeTest1 .................... Passed 0.05 sec test 176 Start 176: molInterchangeCatchTest 176: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 176: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 176: Test timeout computed to be: 1500 176: Randomness seeded to: 4286404160 176: [04:49:05] unrecognized bond type 12 set to zero while writing 176: [04:49:05] unrecognized bond type 0 set to zero while writing 176: =============================================================================== 176: All tests passed (117 assertions in 5 test cases) 176: 165/223 Test #176: molInterchangeCatchTest ................ Passed 0.06 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-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 177: Test timeout computed to be: 1500 171: iterative 177: .. 177: ---------------------------------------------------------------------- 177: Ran 2 tests in 0.015s 177: 177: OK 166/223 Test #177: pyMolInterchange ....................... Passed 0.84 sec test 178 Start 178: testSLNParse 178: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 178: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse 178: Test timeout computed to be: 1500 178: [04:49:05] SLN Parse Error: syntax error while parsing: CH4[I=13] 178: [04:49:05] Failed parsing SLN 'CH4[I=13]' 178: [04:49:05] SLN Parser error: Atom ID 1 appears *after* its ring closure. 178: [04:49:05] SLN Parser error: Ring closure 1 does not have a corresponding opener. 178: [04:49:05] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) 178: [04:49:05] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' 178: [04:49:05] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) 178: [04:49:05] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' 178: [04:49:05] SLN Parse Error: syntax error while parsing: CH4 fff 178: [04:49:05] Failed parsing SLN 'CH4 fff' 178: [04:49:05] SLN Parse Error: syntax error while parsing: C[charge=+1] foo 178: [04:49:05] Failed parsing SLN 'C[charge=+1] foo' 178: [04:49:05] Query property 'is' ignored on non-query atom 178: [04:49:05] Query property 'is' ignored on non-query atom 167/223 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-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 179: Test timeout computed to be: 1500 179: .. 179: ---------------------------------------------------------------------- 179: Ran 2 tests in 0.030s 179: 179: OK 168/223 Test #179: pySLNParse ............................. Passed 0.86 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-aarch64-linux-gnu/Code/GraphMol/Wrap 180: Test timeout computed to be: 1500 174: .................. 174: ---------------------------------------------------------------------- 174: Ran 18 tests in 1.836s 174: 174: OK 169/223 Test #174: pyRGroupDecomposition .................. Passed 2.61 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-aarch64-linux-gnu/Code/GraphMol/Wrap 181: Test timeout computed to be: 1500 180: ..............[04:49:07] SMARTS Parse Error: syntax error while parsing: fiib 180: [04:49:07] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' 171: bulk 180: ....[04:49:07] ERROR: Problems encountered parsing data fields 180: [04:49:07] ERROR: moving to the beginning of the next molecule 180: [04:49:07] ERROR: Problems encountered parsing data fields 180: [04:49:07] ERROR: moving to the beginning of the next molecule 180: [04:49:07] Spurious data before the first property will be ignored 180: [04:49:07] Property will be truncated after the first blank line 180: [04:49:07] Property will be truncated after the first blank line 180: [04:49:07] Property will be truncated after the first blank line 180: [04:49:07] ERROR: Problems encountered parsing data fields 180: [04:49:07] ERROR: moving to the beginning of the next molecule 180: [04:49:07] ERROR: Problems encountered parsing data fields 180: [04:49:07] ERROR: moving to the beginning of the next molecule 180: [04:49:07] Spurious data before the first property will be ignored 180: [04:49:07] Property will be truncated after the first blank line 180: [04:49:07] Property will be truncated after the first blank line 180: [04:49:07] Property will be truncated after the first blank line 180: [04:49:07] ERROR: Problems encountered parsing data fields 180: [04:49:07] ERROR: moving to the beginning of the next molecule 180: [04:49:07] Property will be truncated after the first blank line 180: [04:49:07] ERROR: Problems encountered parsing data fields 180: [04:49:07] ERROR: moving to the beginning of the next molecule 180: [04:49:07] Property will be truncated after the first blank line 180: .[04:49:07] SMILES Parse Error: syntax error while parsing: fail 180: [04:49:07] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' 180: [04:49:07] ERROR: Smiles parse error on line 2 180: [04:49:07] ERROR: Cannot create molecule from : 'fail' 180: >>> This may result in an infinite loop. It should finish almost instantly 180: <<< OK, it finished. 135: ......[04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: .[04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: .[04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: [04:49:07] Molecule does not have explicit Hs. Consider calling AddHs() 135: . 135: ---------------------------------------------------------------------- 135: Ran 19 tests in 32.588s 135: 135: OK 180: ............[04:49:07] Explicit valence for atom # 1 C, 5, is greater than permitted 180: ............[04:49:07] non-ring atom 0 marked aromatic 180: [04:49:07] non-ring atom 0 marked aromatic 180: [04:49:07] 180: 180: **** 180: Range Error 180: idx 180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp 180: Failed Expression: 12 < 6 180: **** 180: 180: [04:49:07] non-ring atom 0 marked aromatic 180: [04:49:07] non-ring atom 0 marked aromatic 180: [04:49:07] 180: 180: **** 180: Range Error 180: idx 180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp 180: Failed Expression: 12 < 6 180: **** 180: 180: ...............[04:49:07] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. 180: [04:49:07] 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. 170/223 Test #135: pyDistGeomHelpers ...................... Passed 33.52 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-aarch64-linux-gnu/Code/GraphMol/Wrap 182: Test timeout computed to be: 1500 180: ..............[04:49:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 180: [04:49:07] Explicit valence for atom # 1 C, 5, is greater than permitted 181: ...... 181: ---------------------------------------------------------------------- 181: Ran 6 tests in 0.021s 181: 181: OK 171/223 Test #181: pyTestConformerWrap .................... Passed 0.62 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-aarch64-linux-gnu/Code/GraphMol/Wrap 183: Test timeout computed to be: 1500 183: ............. 183: ---------------------------------------------------------------------- 183: Ran 13 tests in 0.046s 183: 183: OK 183: Testing SubstanceGroups wrapper 182: [04:49:08] 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: .[04:49:08] 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: 172/223 Test #183: pyTestSGroups .......................... Passed 0.83 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-aarch64-linux-gnu/Code/GraphMol/Wrap 184: Test timeout computed to be: 1500 182: .[04:49:09] 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: .[04:49:09] 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: ..[04:49:09] 182: 182: **** 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: .[04:49:09] 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: [04:49:09] 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: .[04:49:09] 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: 182: [04:49:09] 182: 182: **** 182: Range Error 182: pointNum 182: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: 10 < 10 182: **** 182: 182: .[04:49:09] 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: 182: [04:49:09] 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() == 2 182: **** 182: 182: [04:49:09] 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() == 2 182: **** 182: 182: . 182: ---------------------------------------------------------------------- 182: Ran 9 tests in 0.781s 182: 182: OK 182: Testing Trajectory wrapper 173/223 Test #182: pyTestTrajectory ....................... Passed 2.03 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-aarch64-linux-gnu/Code/GraphMol/Wrap 185: Test timeout computed to be: 1500 171: bulk, no symmetry 185: .s. 185: ---------------------------------------------------------------------- 185: Ran 3 tests in 0.158s 185: 185: OK (skipped=1) 185: Testing Smiles and SD MultithreadedMolSupplier 174/223 Test #185: pyTestMultithreadedMolSupplier ......... Passed 1.02 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-aarch64-linux-gnu/Code/GraphMol/Wrap 186: Test timeout computed to be: 1500 186: [04:49:11] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 186: [04:49:11] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 186: [04:49:11] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 186: .[04:49:11] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 186: [04:49:11] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 186: [04:49:11] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 186: ...[04:49:11] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. 186: [04:49:11] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. 186: [04:49:11] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 186: . 186: ---------------------------------------------------------------------- 186: Ran 5 tests in 0.029s 186: 186: OK 175/223 Test #186: pyTestPropertyLists .................... Passed 0.81 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-aarch64-linux-gnu/Code/GraphMol/Wrap 187: Test timeout computed to be: 1500 171: [04:49:11] Relabelling existing label 187: . 187: ---------------------------------------------------------------------- 187: Ran 1 test in 0.014s 187: 187: OK 176/223 Test #187: pyCDXMLTest ............................ Passed 0.56 sec test 188 Start 188: molStandardizeTest 188: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 188: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 188: Test timeout computed to be: 1500 171: Best mapping 177/223 Test #171: testRGroupDecomp ....................... Passed 10.95 sec test 189 Start 189: molNormalizeTest 189: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 189: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 189: Test timeout computed to be: 1500 189: [04:49:12] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 189: [04:49:12] Initializing Normalizer 189: [04:49:12] Running Normalizer 189: [04:49:12] Rule applied: BrokenazidetoN=N+=N- 189: [04:49:12] Initializing Normalizer 189: [04:49:12] Running Normalizer 189: [04:49:12] Initializing Normalizer 189: [04:49:12] Running Normalizer 178/223 Test #189: molNormalizeTest ....................... Passed 0.09 sec test 190 Start 190: molValidateTest 190: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 190: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 190: Test timeout computed to be: 1500 179/223 Test #190: molValidateTest ........................ Passed 0.06 sec test 191 Start 191: molChargeTest 191: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 191: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 191: Test timeout computed to be: 1500 180/223 Test #191: molChargeTest .......................... Passed 0.20 sec test 192 Start 192: molTautomerTest 192: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 192: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 192: Test timeout computed to be: 1500 192: [04:49:13] Tautomer enumeration stopped at 292 tautomers: max transforms reached 181/223 Test #188: molStandardizeTest ..................... Passed 1.61 sec test 193 Start 193: molStandardizeSmallTest 193: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 193: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 193: Test timeout computed to be: 1500 192: [04:49:13] Tautomer enumeration stopped at 292 tautomers: max transforms reached 182/223 Test #193: molStandardizeSmallTest ................ Passed 0.08 sec test 194 Start 194: molFragmentTest 194: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 194: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 194: Test timeout computed to be: 1500 192: [04:49:13] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 194: [04:49:13] SMARTS Parse Error: syntax error while parsing: [Cl 194: [04:49:13] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' 183/223 Test #194: molFragmentTest ........................ Passed 0.10 sec test 195 Start 195: molStandardizeCatchTest 195: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 195: Test timeout computed to be: 1500 192: [04:49:14] Tautomer enumeration stopped at 119 tautomers: canceled 192: Enumeration was canceled due to timeout (50 ms) 195: Randomness seeded to: 2490390649 195: * - * - * - * m1 195: * - * - * - * m2 195: * - * - * - * m1 195: * - * - * - * m2 195: [04:49:14] Can't kekulize mol. Unkekulized atoms: 3 7 195: [04:49:14] Can't kekulize mol. Unkekulized atoms: 3 8 195: [04:49:14] Can't kekulize mol. Unkekulized atoms: 2 3 4 192: 375 192: Enumeration has completed 192: [04:49:14] Tautomer enumeration stopped at 69 tautomers: canceled 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 180: ...........................[04:49:15] unable to set wavy bonds for double bonds: 3 180: .........[04:49:15] 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: 184/223 Test #192: molTautomerTest ........................ Passed 2.91 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-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 196: Test timeout computed to be: 1500 196: .....[04:49:16] Tautomer enumeration stopped at 292 tautomers: max transforms reached 196: [04:49:16] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 196: .[04:49:16] Tautomer enumeration stopped at 88 tautomers: canceled 196: Enumeration was canceled due to timeout (50 ms) 180: ...................[04:49:16] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:16] Explicit valence for atom # 6 F, 2, is greater than permitted 180: [04:49:16] Can't kekulize mol. Unkekulized atoms: 3 4 5 180: ...............[04:49:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 195: =============================================================================== 195: All tests passed (18691 assertions in 41 test cases) 195: 185/223 Test #195: molStandardizeCatchTest ................ Passed 3.39 sec test 197 Start 197: testScaffoldNetwork 197: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 197: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork 197: Test timeout computed to be: 1500 196: Enumeration has completed 196: [04:49:17] Tautomer enumeration stopped at 63 tautomers: canceled 196: ....................[04:49:18] Explicit valence for atom # 1 O, 3, is greater than permitted 196: . 196: ---------------------------------------------------------------------- 196: Ran 27 tests in 1.879s 196: 196: OK 196: done 186/223 Test #196: pyMolStandardize ....................... Passed 2.59 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-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 198: Test timeout computed to be: 1500 197: Randomness seeded to: 662075326 197: =============================================================================== 197: All tests passed (269 assertions in 19 test cases) 197: 187/223 Test #197: testScaffoldNetwork .................... Passed 1.07 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-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 199: Test timeout computed to be: 1500 198: ....... 198: ---------------------------------------------------------------------- 198: Ran 7 tests in 0.024s 198: 198: OK 188/223 Test #198: pyScaffoldNetwork ...................... Passed 0.33 sec test 200 Start 200: testMolEnumerator 200: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 200: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 200: Test timeout computed to be: 1500 200: Randomness seeded to: 3042969149 200: [04:49:18] can only enumerate SRUs with CONNECT=HT or CONNECT=HH 200: =============================================================================== 200: All tests passed (321 assertions in 16 test cases) 200: 189/223 Test #200: testMolEnumerator ...................... Passed 0.06 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-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 201: Test timeout computed to be: 1500 199: . 199: ---------------------------------------------------------------------- 199: Ran 1 test in 0.009s 199: 199: OK 190/223 Test #199: pyScaffoldNetworkPickling .............. Passed 0.45 sec test 202 Start 202: testAbbreviations 202: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 202: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 202: Test timeout computed to be: 1500 202: Randomness seeded to: 2244489904 202: [04:49:18] SMARTS Parse Error: syntax error while parsing: *fail 202: [04:49:18] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' 202: [04:49:18] no suitable SubstanceGroups found 202: =============================================================================== 202: All tests passed (195 assertions in 12 test cases) 202: 191/223 Test #202: testAbbreviations ...................... Passed 0.04 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-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 203: Test timeout computed to be: 1500 201: ... 201: ---------------------------------------------------------------------- 201: Ran 3 tests in 0.016s 201: 201: OK 192/223 Test #201: pyMolEnumerator ........................ Passed 0.54 sec test 204 Start 204: generalizedSubstructCatch 204: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 204: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 204: Test timeout computed to be: 1500 203: ....... 203: ---------------------------------------------------------------------- 203: Ran 7 tests in 0.029s 203: 203: OK 193/223 Test #203: pyAbbreviations ........................ Passed 0.58 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-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 205: Test timeout computed to be: 1500 204: Randomness seeded to: 1851950427 204: =============================================================================== 204: All tests passed (180 assertions in 10 test cases) 204: 194/223 Test #204: generalizedSubstructCatch .............. Passed 0.28 sec test 206 Start 206: testQuery 206: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Query/testQuery 206: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Query 206: Test timeout computed to be: 1500 206: Query 206: Query2 206: Equality 206: Greater 206: GreaterEqual 206: Less 206: LessEqual 206: Open Range 206: Closed Range 206: Float 206: With Tolerance 206: Set 206: And 206: Or 206: XOr 206: pointer and copy foo 206: Set2 195/223 Test #206: testQuery .............................. Passed 0.02 sec test 207 Start 207: testMatCalc 207: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 207: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc 207: Test timeout computed to be: 1500 207: 1.68022e+08 207: 1.73149e+08 207: 1.05549e+08 207: 7.20603e+07 207: 1.41535e+08 207: 1.08592e+08 207: 1.11334e+08 207: 2.05553e+08 207: 1.54962e+08 207: 8.08231e+07 207: 5.61421e+07 207: 1.28874e+08 207: 1.59011e+08 207: 8.69902e+07 207: 1.31367e+08 207: 2.27389e+08 207: 1.60289e+08 207: 7.79813e+07 207: 1.61001e+08 207: 2.07599e+08 207: 2.24432e+08 207: 1.39725e+08 207: 2.42614e+08 207: 1.77578e+08 207: 1.05908e+08 207: 9.06742e+07 207: 1.8087e+08 207: 1.98182e+08 207: 2.03052e+08 207: 1.7673e+08 207: 9.32798e+07 207: 1.37969e+08 207: 1.83778e+08 207: 2.1228e+08 207: 5.06157e+07 207: 1.566e+08 207: 2.37142e+08 207: 1.49345e+08 207: 7.05819e+07 207: 1.71633e+08 207: 1.96817e+08 207: 2.18246e+08 207: 9.49496e+07 207: 2.25618e+08 207: 1.30219e+08 196/223 Test #207: testMatCalc ............................ Passed 0.03 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-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 208: Test timeout computed to be: 1500 205: ....... 205: ---------------------------------------------------------------------- 205: Ran 7 tests in 0.215s 205: 205: OK 197/223 Test #205: pyGeneralizedSubstruct ................. Passed 0.83 sec test 209 Start 209: testSimDivPickers 209: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 209: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers 209: Test timeout computed to be: 1500 209: [04:49:20] ------------------------------------- 209: [04:49:20] Testing github issue 1421: MaxMinPicker picking non-existent element. 209: [04:49:20] Done 209: [04:49:20] ------------------------------------- 209: [04:49:20] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. 209: [04:49:20] Done 198/223 Test #209: testSimDivPickers ...................... Passed 0.01 sec test 210 Start 210: pickersTestsCatch 210: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 210: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers 210: Test timeout computed to be: 1500 210: Randomness seeded to: 4280052364 210: =============================================================================== 210: All tests passed (21267 assertions in 1 test case) 210: 199/223 Test #210: pickersTestsCatch ...................... Passed 0.11 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-aarch64-linux-gnu/Code/SimDivPickers/Wrap 211: Test timeout computed to be: 1500 208: ..... 208: ---------------------------------------------------------------------- 208: Ran 5 tests in 0.449s 208: 208: OK 200/223 Test #208: pyMatCalc .............................. Passed 1.16 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-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 212: Test timeout computed to be: 1500 211: [04:49:20] the useCache argument is deprecated and ignored 170: ......[04:49:20] 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: [04:49:20] 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: 211: ...[04:49:21] the useCache argument is deprecated and ignored 211: [04:49:21] the useCache argument is deprecated and ignored 211: .[04:49:21] the useCache argument is deprecated and ignored 212: ..[04:49:21] 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 0.028s 212: 212: OK 201/223 Test #212: pyRanker ............................... Passed 0.54 sec test 213 Start 213: testChemicalFeatures 213: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 213: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures 213: Test timeout computed to be: 1500 213: ----------------------------------------- 213: Test1 213: Done 202/223 Test #213: testChemicalFeatures ................... Passed 0.02 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-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap 214: Test timeout computed to be: 1500 203/223 Test #184: pyTestThreads .......................... Passed 12.81 sec test 215 Start 215: pythonTestDbCLI 215: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/Projects" 215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Projects 215: Test timeout computed to be: 1500 214: .. 214: ---------------------------------------------------------------------- 214: Ran 2 tests in 0.001s 214: 214: OK 214: Testing ChemicalFeatures Wrapper code: 211: ....... 211: ---------------------------------------------------------------------- 211: Ran 11 tests in 1.381s 211: 211: OK 204/223 Test #214: pyFeatures ............................. Passed 0.93 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-aarch64-linux-gnu/rdkit 216: Test timeout computed to be: 1500 205/223 Test #211: pySimDivPickers ........................ Passed 1.84 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-aarch64-linux-gnu/rdkit 217: Test timeout computed to be: 1500 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML import BuildComposite 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) 215: [04:49:23] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:23] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:23] INFO: Processing 10 molecules 215: 215: [04:49:23] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:23] INFO: Finished. 215: 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) 217: . 217: ---------------------------------------------------------------------- 217: Ran 6 tests in 0.638s 217: 217: OK 216: ......................... 216: ---------------------------------------------------------------------- 216: Ran 25 tests in 1.117s 216: 216: OK 206/223 Test #216: pythonTestDirRoot ...................... Passed 1.62 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-aarch64-linux-gnu/rdkit 218: Test timeout computed to be: 1500 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 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) 180: ..[04:49:24] 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: [04:49:24] 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: [04:49:24] 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: [04:49:24] 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: [04:49:24] 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: .....[04:49:24] 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: 180: ......[04:49:24] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 180: [04:49:24] ERROR: Smiles parse error on line 0 180: [04:49:24] ERROR: Cannot create molecule from : 'c1ccccc' 180: [04:49:24] SMILES Parse Error: extra open parentheses for input: 'C(C' 180: [04:49:24] ERROR: Smiles parse error on line 3 180: [04:49:24] ERROR: Cannot create molecule from : 'C(C' 180: [04:49:24] Explicit valence for atom # 1 C, 5, is greater than permitted 180: [04:49:24] ERROR: Could not sanitize molecule on line 6 180: [04:49:24] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted 180: [04:49:24] SMILES Parse Error: unclosed ring for input: 'c1ccccc' 180: [04:49:24] ERROR: Smiles parse error on line 0 180: [04:49:24] ERROR: Cannot create molecule from : 'c1ccccc' 180: [04:49:24] SMILES Parse Error: extra open parentheses for input: 'C(C' 180: [04:49:24] ERROR: Smiles parse error on line 3 180: [04:49:24] ERROR: Cannot create molecule from : 'C(C' 180: [04:49:24] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' 180: [04:49:24] ERROR: Smiles parse error on line 6 180: [04:49:24] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' 180: [04:49:24] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:24] ERROR: Could not sanitize molecule ending on line 21 180: [04:49:24] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:24] ERROR: EOF hit while reading atoms 180: [04:49:24] ERROR: moving to the beginning of the next molecule 180: [04:49:24] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:24] ERROR: Could not sanitize molecule ending on line 21 180: [04:49:24] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:24] ERROR: EOF hit while reading atoms 180: [04:49:24] ERROR: moving to the beginning of the next molecule 180: ....[04:49:24] 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: ..........[04:49:24] 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: ..[04:49:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 217: .......... 217: ---------------------------------------------------------------------- 217: Ran 12 tests in 0.317s 217: 217: OK 218: ....... 218: ---------------------------------------------------------------------- 218: Ran 7 tests in 0.031s 218: 218: OK 180: ..........................[04:49:24] SMILES Parse Error: unclosed ring for input: 'C1CC' 180: ......[04:49:24] WARNING: not removing hydrogen atom without neighbors 180: [04:49:24] WARNING: not removing hydrogen atom with dummy atom neighbors 180: [04:49:24] WARNING: not removing hydrogen atom with wedged bond 180: [04:49:24] WARNING: not removing hydrogen atom without neighbors 180: [04:49:24] WARNING: not removing hydrogen atom with dummy atom neighbors 137: --------------------------------- 137: test getO3AForProbeConfs 137: 137: *********************************************************** 207/223 Test #137: testO3AAlign ........................... Passed 50.51 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-aarch64-linux-gnu/rdkit 219: Test timeout computed to be: 1500 180: .....[04:49:25] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 180: .[04:49:25] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:25] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:25] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:25] Explicit valence for atom # 1 F, 2, is greater than permitted 180: [04:49:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 180: [04:49:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 180: [04:49:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 217: /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 180: ..........[04:49:25] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 180: [04:49:25] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 180: .[04:49:25] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname 180: [04:49:25] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' 180: ..[04:49:25] SMILES Parse Error: syntax error while parsing: error 180: [04:49:25] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' 180: [04:49:25] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' 180: [04:49:25] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' 180: [04:49:25] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' 180: ................[04:49:25] SMILES Parse Error: syntax error while parsing: garbage_0 180: [04:49:25] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' 180: [04:49:25] SMILES Parse Error: syntax error while parsing: garbage_2 180: [04:49:25] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' 180: [04:49:25] SMILES Parse Error: syntax error while parsing: garbage_4 180: [04:49:25] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 180: .......... 180: ---------------------------------------------------------------------- 180: Ran 248 tests in 17.671s 180: 180: OK 180: 262 180: supplier: 180: supplier: 180: supplier: 215: [04:49:25] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:25] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:25] INFO: Processing 163 molecules 215: 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 208/223 Test #180: pyGraphMolWrap ......................... Passed 18.61 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-aarch64-linux-gnu/rdkit 220: Test timeout computed to be: 1500 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 218: .................................. 218: ---------------------------------------------------------------------- 218: Ran 34 tests in 0.016s 218: 218: OK 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] 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/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: c1 = pickle.load(pklF) 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] INFO: done 100 215: 219: .. 219: ---------------------------------------------------------------------- 219: Ran 2 tests in 0.027s 219: 219: OK 217: . 217: ---------------------------------------------------------------------- 217: Ran 1 test in 0.063s 217: 217: OK 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:25] INFO: Generating fingerprints and descriptors: 215: 219: ........... 219: ---------------------------------------------------------------------- 219: Ran 11 tests in 0.040s 219: 219: OK 209/223 Test #220: pythonTestDirSimDivFilters ............. Passed 0.76 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-aarch64-linux-gnu/rdkit 221: Test timeout computed to be: 1500 219: . 219: ---------------------------------------------------------------------- 219: Ran 1 test in 0.001s 219: 219: OK 218: ..... 218: ---------------------------------------------------------------------- 218: Ran 5 tests in 0.008s 218: 218: OK 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 0.019s 219: 219: FAILED (failures=3) 217: ... 217: ---------------------------------------------------------------------- 217: Ran 3 tests in 0.009s 217: 217: OK 219: ...... 219: ---------------------------------------------------------------------- 219: Ran 6 tests in 0.003s 219: 219: OK 221: ............. 221: ---------------------------------------------------------------------- 221: Ran 13 tests in 0.024s 221: 221: OK 219: !!! TEST FAILURE: python UnitTestDbUtils.py {} 210/223 Test #219: pythonTestDirDbase .....................***Failed 1.58 sec .. ---------------------------------------------------------------------- Ran 2 tests in 0.027s OK ........... ---------------------------------------------------------------------- Ran 11 tests in 0.040s 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 0.019s FAILED (failures=3) ...... ---------------------------------------------------------------------- Ran 6 tests in 0.003s OK !!! TEST FAILURE: python UnitTestDbUtils.py {} 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-aarch64-linux-gnu/rdkit 222: Test timeout computed to be: 1500 217: ........ 217: ---------------------------------------------------------------------- 217: Ran 8 tests in 0.000s 217: 217: OK 218: ....... 218: ---------------------------------------------------------------------- 218: Ran 7 tests in 0.001s 218: 218: OK 211/223 Test #218: pythonTestDirDataStructs ............... Passed 3.51 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-aarch64-linux-gnu/rdkit/Chem 223: Test timeout computed to be: 1500 221: ........... 221: ---------------------------------------------------------------------- 221: Ran 11 tests in 0.076s 221: 221: 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 222: .. 222: ---------------------------------------------------------------------- 222: Ran 2 tests in 0.188s 222: 222: OK 212/223 Test #222: pythonTestSping ........................ Passed 0.97 sec 213/223 Test #221: pythonTestDirVLib ...................... Passed 1.50 sec 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 223: ....... 223: ---------------------------------------------------------------------- 223: Ran 7 tests in 0.144s 223: 223: OK 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.621s 217: 217: OK 223: ...... 223: ---------------------------------------------------------------------- 223: Ran 6 tests in 0.055s 223: 223: OK 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 0.001s 217: 217: OK 223: ....[04:49:29] 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 0.026s 223: 223: OK 217: ......... 217: ---------------------------------------------------------------------- 217: Ran 9 tests in 0.002s 217: 217: OK 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.010s 223: 223: OK 217: ............ 217: ---------------------------------------------------------------------- 217: Ran 12 tests in 0.009s 217: 217: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.019s 223: 223: OK 134: [04:49:30] UFFTYPER: Unrecognized atom type: S_6+6 (0) 134: [04:49:31] UFFTYPER: Warning: hybridization set to SP3 for atom 0 134: [04:49:31] UFFTYPER: Unrecognized charge state for atom: 0 223: ...................... 223: ---------------------------------------------------------------------- 223: Ran 22 tests in 0.020s 223: 223: OK 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 0.018s 217: 217: OK 215: [04:49:31] INFO: Finished. 215: 223: .....s.................ss 223: ---------------------------------------------------------------------- 223: Ran 25 tests in 0.084s 223: 223: OK (skipped=3) 134: =============================================================================== 134: All tests passed (448 assertions in 10 test cases) 134: 214/223 Test #134: distGeomHelpersCatch ................... Passed 58.74 sec 223: ..s 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.193s 223: 223: OK (skipped=1) 215: .[04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] 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/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import TreeUtils 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: . 217: ---------------------------------------------------------------------- 217: Ran 1 test in 0.000s 217: 217: OK 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] 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 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: ...... 217: ---------------------------------------------------------------------- 217: Ran 6 tests in 0.001s 217: 217: OK 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] 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/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 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: ................................... 223: ---------------------------------------------------------------------- 223: Ran 35 tests in 1.057s 223: 223: OK 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.025s 223: 223: OK 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.740s 217: 217: OK 215: .[04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: . 223: ---------------------------------------------------------------------- 223: Ran 1 test in 0.015s 223: 223: OK 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import ID3 217: ...... 217: ---------------------------------------------------------------------- 217: Ran 6 tests in 0.027s 217: 217: OK 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree 223: ....... 223: ---------------------------------------------------------------------- 223: Ran 7 tests in 0.052s 223: 223: OK 217: .. 217: ---------------------------------------------------------------------- 217: Ran 2 tests in 0.106s 217: 217: OK 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.030s 223: 223: 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 0.019s 217: 217: OK 215: .[04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:36] 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/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 0.098s 217: 217: OK 170: ............. 170: ---------------------------------------------------------------------- 170: Ran 19 tests in 35.821s 170: 170: OK 170: Testing atom rings 170: testing bond rings 170: searching atom rings 170: searching bond rings 170: done 217: .. 217: ---------------------------------------------------------------------- 217: Ran 2 tests in 0.002s 217: 217: OK 223: .ss.ss....... 223: ---------------------------------------------------------------------- 223: Ran 13 tests in 1.124s 223: 223: OK (skipped=4) 215/223 Test #170: pySubstructLibrary ..................... Passed 36.76 sec 217: ..... 217: ---------------------------------------------------------------------- 217: Ran 5 tests in 0.016s 217: 217: OK 223: [04:49:38] Molecule does not have explicit Hs. Consider calling AddHs() 217: ... 217: ---------------------------------------------------------------------- 217: Ran 3 tests in 0.010s 217: 217: OK 223: .[04:49:38] Molecule does not have explicit Hs. Consider calling AddHs() 217: ... 217: ---------------------------------------------------------------------- 217: Ran 3 tests in 0.419s 217: 217: OK 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, 217: ...... 217: ---------------------------------------------------------------------- 217: Ran 6 tests in 0.338s 217: 217: OK 215: ....[04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.Composite import Composite 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.ModelPackage import Packager, PackageUtils 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:72: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: model = pickle.load(modelF) 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: ....... 217: ---------------------------------------------------------------------- 217: Ran 7 tests in 0.202s 217: 217: OK 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/NaiveBayes/UnitTestNB.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.NaiveBayes import CrossValidate 215: [04:49:42] 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 0.014s 217: 217: OK 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestTrainer.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.Neural import Network, Trainers 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: .[04:49:44] 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 2.339s 217: 217: OK 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 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.001s 217: 217: OK 215: .[04:49:45] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:45] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:45] INFO: Processing 10 molecules 215: 215: [04:49:46] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:46] INFO: Finished. 215: 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.000s 217: 217: OK 217: .... 217: ---------------------------------------------------------------------- 217: Ran 4 tests in 0.008s 217: 217: OK 216/223 Test #217: pythonTestDirML ........................ Passed 24.34 sec 215: [04:49:47] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:47] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:47] INFO: Processing 10 molecules 215: 215: [04:49:47] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:47] INFO: Finished. 215: 215: [04:49:48] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:48] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:48] INFO: Processing 10 molecules 215: 215: [04:49:48] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:48] INFO: Finished. 215: 215: [04:49:49] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:49] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:49] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:49] INFO: Finished. 215: 215: [04:49:50] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:50] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:50] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:50] INFO: Finished. 215: 30: [04:49:51] Finished 30: [04:49:51] ------------------------------------- 30: [04:49:51] Test github1843: RWMol.clear() should not destroy ring pointer. 30: [04:49:51] Finished 217/223 Test #30: graphmolTest1 .......................... Passed 87.32 sec 158: =============================================================================== 158: All tests passed (93 assertions in 5 test cases) 158: 218/223 Test #158: testRascalCluster ...................... Passed 68.06 sec 215: .[04:49:52] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 215: 215: [04:49:52] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:52] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:52] INFO: Processing 163 molecules 215: 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] INFO: done 100 215: 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:52] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:53] INFO: Finished. 215: 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: [04:49:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215: .[04:49:56] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:56] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:56] INFO: Processing 10 molecules 215: 215: [04:49:56] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:56] INFO: Finished. 215: 215: [04:49:57] INFO: Reading molecules and constructing molecular database. 215: 215: [04:49:57] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: 215: [04:49:57] INFO: Processing 10 molecules 215: 215: [04:49:57] INFO: Generating fingerprints and descriptors: 215: 215: [04:49:58] INFO: Finished. 215: 215: . 215: ---------------------------------------------------------------------- 215: Ran 12 tests in 36.453s 215: 215: OK 219/223 Test #215: pythonTestDbCLI ........................ Passed 36.86 sec 133: [04:50:04] done 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 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 223: ....................[04:50:17] WARNING: More than one matching pattern found - picking one 223: 223: [04:50:17] WARNING: More than one matching pattern found - picking one 223: 223: .[04:50:17] WARNING: More than one matching pattern found - picking one 223: 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 157: =============================================================================== 157: All tests passed (2552 assertions in 23 test cases) 157: 220/223 Test #157: testRascalMCES ......................... Passed 97.58 sec 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 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 223: ... 223: ---------------------------------------------------------------------- 223: Ran 25 tests in 43.963s 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'] 133: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 223: ........ 223: ---------------------------------------------------------------------- 223: Ran 8 tests in 0.231s 223: 223: OK 223: .[04:50:24] Molecule does not have explicit Hs. Consider calling AddHs() 133: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 133: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 133: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 133: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 133: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 223: F....[04:50:29] WARNING: not removing hydrogen atom without neighbors 223: [04:50:29] WARNING: not removing hydrogen atom without neighbors 223: [04:50:29] WARNING: not removing hydrogen atom without neighbors 223: ....[04:50:29] WARNING: not removing hydrogen atom without neighbors 223: ...... 223: ====================================================================== 223: FAIL: testGet3DMolDescriptors (__main__.TestCase.testGet3DMolDescriptors) 223: ---------------------------------------------------------------------- 223: Traceback (most recent call last): 223: File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestDescriptors.py", line 216, in testGet3DMolDescriptors 223: self.assertEqual(descs['PMI1'], 20.954531335493417) 223: AssertionError: 20.954531335493083 != 20.954531335493417 223: 223: ---------------------------------------------------------------------- 223: Ran 16 tests in 5.185s 223: 223: FAILED (failures=1) 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: [04:50:29] WARNING: Omitted undefined stereo 223: 223: [04:50:29] WARNING: Proton(s) added/removed 223: 133: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 133: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] 133: [04:50:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 133: [04:50:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: ..[04:50:33] ERROR: Add/Remove protons error; *Conversion failed* 223: 223: [04:50:33] 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 3.744s 223: 223: FAILED (errors=1) 223: 223: InChI write Summary: 1160 identical, 0 suffix variance, 21 reasonable 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 1.422s 223: 223: OK 223: ...... 223: ---------------------------------------------------------------------- 223: Ran 6 tests in 0.321s 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 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 0xffffae24f060>
\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 0xffffae24d9a0>NaN
1NaNrtzPeroxide<rdkit.Chem.rdchem.Mol object at 0xffffad6f22d0>yxcv
' 223: 223: ---------------------------------------------------------------------- 223: Ran 28 tests in 2.361s 223: 223: FAILED (failures=2, skipped=2) 133: [04:50:41] Molecule does not have explicit Hs. Consider calling AddHs() 221/223 Test #133: testDistGeomHelpers .................... Passed 128.58 sec 223: ..............[04:50:51] WARNING: More than one matching pattern found - picking one 223: 223: [04:50:51] WARNING: More than one matching pattern found - picking one 223: 223: ..[04:50:51] Molecule does not have explicit Hs. Consider calling AddHs() 223: [04:50:51] Molecule does not have explicit Hs. Consider calling AddHs() 223: [04:50:51] Molecule does not have explicit Hs. Consider calling AddHs() 223: [04:50:51] Molecule does not have explicit Hs. Consider calling AddHs() 223: ......... 223: ---------------------------------------------------------------------- 223: Ran 25 tests in 10.746s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.111s 223: 223: OK 223: ..s... 223: ---------------------------------------------------------------------- 223: Ran 6 tests in 2.025s 223: 223: OK (skipped=1) 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.035s 223: 223: OK 223: .............. 223: ---------------------------------------------------------------------- 223: Ran 14 tests in 8.707s 223: 223: OK 223: ..[04:51:23] WARNING: not removing hydrogen atom without neighbors 223: .[04:51:23] WARNING: not removing hydrogen atom without neighbors 223: .[04:51:23] WARNING: no name column found on line 1 223: [04:51:23] WARNING: no name column found on line 2 223: [04:51:23] WARNING: no name column found on line 3 223: [04:51:23] WARNING: no name column found on line 4 223: [04:51:23] WARNING: no name column found on line 5 223: [04:51:23] WARNING: no name column found on line 6 223: [04:51:23] WARNING: no name column found on line 7 223: [04:51:23] WARNING: no name column found on line 8 223: [04:51:23] WARNING: no name column found on line 9 223: [04:51:23] WARNING: no name column found on line 10 223: [04:51:23] WARNING: no name column found on line 11 223: [04:51:23] WARNING: no name column found on line 12 223: [04:51:23] WARNING: no name column found on line 13 223: [04:51:23] WARNING: no name column found on line 14 223: [04:51:23] WARNING: no name column found on line 15 223: [04:51:23] WARNING: no name column found on line 16 223: [04:51:23] WARNING: no name column found on line 17 223: [04:51:23] WARNING: no name column found on line 18 223: [04:51:23] WARNING: no name column found on line 19 223: [04:51:23] WARNING: no name column found on line 20 223: [04:51:23] WARNING: no name column found on line 21 223: [04:51:23] WARNING: no name column found on line 22 223: [04:51:23] WARNING: no name column found on line 23 223: [04:51:23] WARNING: no name column found on line 24 223: [04:51:23] WARNING: no name column found on line 25 223: [04:51:23] WARNING: no name column found on line 26 223: [04:51:23] WARNING: no name column found on line 27 223: [04:51:23] WARNING: no name column found on line 28 223: [04:51:23] WARNING: no name column found on line 29 223: [04:51:23] WARNING: no name column found on line 30 223: [04:51:23] WARNING: no name column found on line 31 223: [04:51:23] WARNING: no name column found on line 32 223: [04:51:23] WARNING: no name column found on line 33 223: [04:51:23] WARNING: no name column found on line 34 223: [04:51:23] WARNING: no name column found on line 35 223: [04:51:23] WARNING: no name column found on line 36 223: [04:51:23] WARNING: no name column found on line 37 223: [04:51:23] WARNING: no name column found on line 38 223: [04:51:23] WARNING: no name column found on line 39 223: [04:51:23] WARNING: no name column found on line 40 223: [04:51:23] WARNING: no name column found on line 41 223: [04:51:23] WARNING: no name column found on line 42 223: [04:51:23] WARNING: no name column found on line 43 223: [04:51:23] WARNING: no name column found on line 44 223: [04:51:23] WARNING: no name column found on line 45 223: [04:51:23] WARNING: no name column found on line 46 223: [04:51:23] WARNING: no name column found on line 47 223: [04:51:23] WARNING: no name column found on line 48 223: [04:51:23] WARNING: no name column found on line 49 223: [04:51:23] WARNING: no name column found on line 50 223: [04:51:23] WARNING: no name column found on line 51 223: [04:51:23] WARNING: no name column found on line 52 223: [04:51:23] WARNING: no name column found on line 53 223: [04:51:23] WARNING: no name column found on line 54 223: [04:51:23] WARNING: no name column found on line 55 223: [04:51:23] WARNING: no name column found on line 56 223: [04:51:23] WARNING: no name column found on line 57 223: [04:51:23] WARNING: no name column found on line 58 223: [04:51:23] WARNING: no name column found on line 59 223: [04:51:23] WARNING: no name column found on line 60 223: [04:51:23] WARNING: no name column found on line 61 223: [04:51:23] WARNING: no name column found on line 62 223: [04:51:23] WARNING: no name column found on line 63 223: [04:51:23] WARNING: no name column found on line 64 223: [04:51:23] WARNING: no name column found on line 65 223: [04:51:23] WARNING: no name column found on line 66 223: [04:51:23] WARNING: no name column found on line 67 223: [04:51:23] WARNING: no name column found on line 68 223: [04:51:23] WARNING: no name column found on line 69 223: [04:51:23] WARNING: no name column found on line 70 223: [04:51:23] WARNING: no name column found on line 71 223: [04:51:23] WARNING: no name column found on line 72 223: [04:51:23] WARNING: no name column found on line 73 223: [04:51:23] WARNING: no name column found on line 74 223: [04:51:23] WARNING: no name column found on line 75 223: [04:51:23] WARNING: no name column found on line 76 223: [04:51:23] WARNING: no name column found on line 77 223: [04:51:23] WARNING: no name column found on line 78 223: [04:51:23] WARNING: no name column found on line 79 223: [04:51:23] WARNING: no name column found on line 80 223: [04:51:23] WARNING: no name column found on line 81 223: [04:51:23] WARNING: no name column found on line 82 223: [04:51:23] WARNING: no name column found on line 83 223: [04:51:23] WARNING: no name column found on line 84 223: [04:51:23] WARNING: no name column found on line 85 223: [04:51:23] WARNING: no name column found on line 86 223: [04:51:23] WARNING: no name column found on line 87 223: [04:51:23] WARNING: no name column found on line 88 223: [04:51:23] WARNING: no name column found on line 89 223: [04:51:23] WARNING: no name column found on line 90 223: [04:51:23] WARNING: no name column found on line 91 223: [04:51:23] WARNING: no name column found on line 92 223: [04:51:23] WARNING: no name column found on line 93 223: [04:51:23] WARNING: no name column found on line 94 223: [04:51:23] WARNING: no name column found on line 95 223: [04:51:23] WARNING: no name column found on line 96 223: [04:51:23] WARNING: no name column found on line 97 223: [04:51:23] WARNING: no name column found on line 98 223: [04:51:23] WARNING: no name column found on line 99 223: [04:51:23] WARNING: no name column found on line 100 223: [04:51:23] WARNING: no name column found on line 101 223: [04:51:23] WARNING: no name column found on line 102 223: [04:51:23] WARNING: no name column found on line 103 223: [04:51:23] WARNING: no name column found on line 104 223: [04:51:23] WARNING: no name column found on line 105 223: [04:51:23] WARNING: no name column found on line 106 223: [04:51:23] WARNING: no name column found on line 107 223: [04:51:23] WARNING: no name column found on line 108 223: [04:51:23] WARNING: no name column found on line 109 223: [04:51:23] WARNING: no name column found on line 110 223: [04:51:23] WARNING: no name column found on line 111 223: [04:51:23] WARNING: no name column found on line 112 223: [04:51:23] WARNING: no name column found on line 113 223: [04:51:23] WARNING: no name column found on line 114 223: [04:51:23] WARNING: no name column found on line 115 223: [04:51:23] WARNING: no name column found on line 116 223: [04:51:23] WARNING: no name column found on line 117 223: [04:51:23] WARNING: no name column found on line 118 223: [04:51:23] WARNING: no name column found on line 119 223: [04:51:23] WARNING: no name column found on line 120 223: [04:51:23] WARNING: no name column found on line 121 223: [04:51:23] WARNING: no name column found on line 122 223: [04:51:23] WARNING: no name column found on line 123 223: [04:51:23] WARNING: no name column found on line 124 223: [04:51:23] WARNING: no name column found on line 125 223: [04:51:23] WARNING: no name column found on line 126 223: [04:51:23] WARNING: no name column found on line 127 223: [04:51:23] WARNING: no name column found on line 128 223: [04:51:23] WARNING: no name column found on line 129 223: [04:51:23] WARNING: no name column found on line 130 223: [04:51:23] WARNING: no name column found on line 131 223: [04:51:23] WARNING: no name column found on line 132 223: [04:51:23] WARNING: no name column found on line 133 223: [04:51:23] WARNING: no name column found on line 134 223: [04:51:23] WARNING: no name column found on line 135 223: [04:51:23] WARNING: no name column found on line 136 223: [04:51:23] WARNING: no name column found on line 137 223: [04:51:23] WARNING: no name column found on line 138 223: [04:51:23] WARNING: no name column found on line 139 223: [04:51:23] WARNING: no name column found on line 140 223: [04:51:23] WARNING: no name column found on line 141 223: [04:51:23] WARNING: no name column found on line 142 223: [04:51:23] WARNING: no name column found on line 143 223: [04:51:23] WARNING: no name column found on line 144 223: [04:51:23] WARNING: no name column found on line 145 223: [04:51:23] WARNING: no name column found on line 146 223: [04:51:23] WARNING: no name column found on line 147 223: [04:51:23] WARNING: no name column found on line 148 223: [04:51:23] WARNING: no name column found on line 149 223: [04:51:23] WARNING: no name column found on line 150 223: [04:51:23] WARNING: no name column found on line 151 223: [04:51:23] WARNING: no name column found on line 152 223: [04:51:23] WARNING: no name column found on line 153 223: [04:51:23] WARNING: no name column found on line 154 223: [04:51:23] WARNING: no name column found on line 155 223: [04:51:23] WARNING: no name column found on line 156 223: [04:51:23] WARNING: no name column found on line 157 223: [04:51:23] WARNING: no name column found on line 158 223: [04:51:23] WARNING: no name column found on line 159 223: [04:51:23] WARNING: no name column found on line 160 223: [04:51:23] WARNING: no name column found on line 161 223: [04:51:23] WARNING: no name column found on line 162 223: [04:51:23] WARNING: no name column found on line 163 223: [04:51:23] WARNING: no name column found on line 164 223: [04:51:23] WARNING: no name column found on line 165 223: [04:51:23] WARNING: no name column found on line 166 223: [04:51:23] WARNING: no name column found on line 167 223: [04:51:23] WARNING: no name column found on line 168 223: [04:51:23] WARNING: no name column found on line 169 223: [04:51:23] WARNING: no name column found on line 170 223: [04:51:23] WARNING: no name column found on line 171 223: [04:51:23] WARNING: no name column found on line 172 223: [04:51:23] WARNING: no name column found on line 173 223: [04:51:23] WARNING: no name column found on line 174 223: [04:51:23] WARNING: no name column found on line 175 223: [04:51:23] WARNING: no name column found on line 176 223: [04:51:23] WARNING: no name column found on line 177 223: [04:51:23] WARNING: no name column found on line 178 223: [04:51:23] WARNING: no name column found on line 179 223: [04:51:23] WARNING: no name column found on line 180 223: [04:51:23] WARNING: no name column found on line 181 223: [04:51:23] WARNING: no name column found on line 182 223: [04:51:23] WARNING: no name column found on line 183 223: [04:51:23] WARNING: no name column found on line 184 223: [04:51:23] WARNING: no name column found on line 185 223: [04:51:23] WARNING: no name column found on line 186 223: [04:51:23] WARNING: no name column found on line 187 223: [04:51:23] WARNING: no name column found on line 188 223: [04:51:23] WARNING: no name column found on line 189 223: [04:51:23] WARNING: no name column found on line 190 223: [04:51:23] WARNING: no name column found on line 191 223: [04:51:23] WARNING: no name column found on line 192 223: [04:51:23] WARNING: no name column found on line 193 223: [04:51:23] WARNING: no name column found on line 194 223: [04:51:23] WARNING: no name column found on line 195 223: [04:51:23] WARNING: no name column found on line 196 223: [04:51:23] WARNING: no name column found on line 197 223: [04:51:23] WARNING: no name column found on line 198 223: [04:51:23] WARNING: no name column found on line 199 223: [04:51:23] WARNING: no name column found on line 200 223: [04:51:23] WARNING: no name column found on line 201 223: [04:51:23] WARNING: no name column found on line 202 223: [04:51:23] WARNING: no name column found on line 203 223: [04:51:23] WARNING: no name column found on line 204 223: [04:51:23] WARNING: no name column found on line 205 223: [04:51:23] WARNING: no name column found on line 206 223: [04:51:23] WARNING: no name column found on line 207 223: [04:51:23] WARNING: no name column found on line 208 223: [04:51:23] WARNING: no name column found on line 209 223: [04:51:23] WARNING: no name column found on line 210 223: [04:51:23] WARNING: no name column found on line 211 223: [04:51:23] WARNING: no name column found on line 212 223: [04:51:23] WARNING: no name column found on line 213 223: [04:51:23] WARNING: no name column found on line 214 223: [04:51:23] WARNING: no name column found on line 215 223: [04:51:23] WARNING: no name column found on line 216 223: ...... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.149s 223: 223: OK 223: .................. 223: ---------------------------------------------------------------------- 223: Ran 18 tests in 2.000s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.224s 223: 223: OK 223: ........ 223: ---------------------------------------------------------------------- 223: Ran 8 tests in 0.072s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.046s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.024s 223: 223: OK 223: . 223: ---------------------------------------------------------------------- 223: Ran 1 test in 0.115s 223: 223: OK 223: ........ 223: ---------------------------------------------------------------------- 223: Ran 8 tests in 0.001s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.008s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.005s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.006s 223: 223: OK 223: ....... 223: ---------------------------------------------------------------------- 223: Ran 7 tests in 0.034s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.032s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 3.802s 223: 223: OK 223: .......... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.034s 223: 223: OK 223: . 223: ---------------------------------------------------------------------- 223: Ran 1 test in 0.000s 223: 223: OK 223: .......... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.003s 223: 223: OK 223: ..... 223: ---------------------------------------------------------------------- 223: Ran 5 tests in 0.050s 223: 223: OK 223: .........[04:51:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: [04:51:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: [04:51:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: [04:51:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: .......[04:51:55] Molecule does not have explicit Hs. Consider calling AddHs() 223: [04:51:55] Molecule does not have explicit Hs. Consider calling AddHs() 223: ..... 223: ---------------------------------------------------------------------- 223: Ran 21 tests in 9.553s 223: 223: OK 223: mol_197 223: 219.68,35.94,110.98,11.56,110.32,11.04,95.23,10.25,0.00 223: mol_223 223: 243.69,7.04,134.64,0.81,134.56,0.81,85.50,0.37,0.00 223: mol_269 223: 216.59,3.99,105.00,0.87,103.81,0.89,89.27,0.92,6.00 223: . 223: ---------------------------------------------------------------------- 223: Ran 1 test in 0.000s 223: 223: OK 223: ...[04:51:57] 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 0.054s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 10.827s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- 223: Ran 2 tests in 0.133s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- 223: Ran 3 tests in 0.016s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.013s 223: 223: OK 223: .....[04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: [04:52:12] WARNING: not removing hydrogen atom without neighbors 223: ..... 223: ---------------------------------------------------------------------- 223: Ran 10 tests in 0.467s 223: 223: OK 223: ssssss..........s/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 3.535s 223: 223: OK (skipped=7) 223: sss. 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.526s 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 0.439s 223: 223: OK 223: ...[04:52:20] SMARTS Parse Error: syntax error while parsing: boromicacid 223: [04:52:20] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 223: [04:52:20] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide 223: [04:52:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' 223: [04:52:20] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride 223: [04:52:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' 223: [04:52:20] reaction has no reactants 223: [04:52:20] reaction has no products 223: [04:52:20] initialization failed 223: [04:52:20] reaction has no reactants 223: [04:52:20] reaction has no products 223: . 223: ---------------------------------------------------------------------- 223: Ran 4 tests in 0.020s 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 0.007s 223: 223: OK 223: ........................ 223: ---------------------------------------------------------------------- 223: Ran 24 tests in 0.047s 223: 223: OK 223: !!! TEST FAILURE: python UnitTestDescriptors.py {} 223: !!! TEST FAILURE: python UnitTestInchi.py {} 223: !!! TEST FAILURE: python UnitTestPandasTools.py {} 222/223 Test #223: pythonTestDirChem ......................***Failed 173.73 sec ....... ---------------------------------------------------------------------- Ran 7 tests in 0.144s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.055s OK ....[04:49:29] **** 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 0.026s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.010s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.019s OK ...................... ---------------------------------------------------------------------- Ran 22 tests in 0.020s OK .....s.................ss ---------------------------------------------------------------------- Ran 25 tests in 0.084s OK (skipped=3) ..s ---------------------------------------------------------------------- Ran 3 tests in 0.193s OK (skipped=1) ................................... ---------------------------------------------------------------------- Ran 35 tests in 1.057s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.025s OK . ---------------------------------------------------------------------- Ran 1 test in 0.015s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.052s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.030s OK .ss.ss....... ---------------------------------------------------------------------- Ran 13 tests in 1.124s OK (skipped=4) [04:49:38] Molecule does not have explicit Hs. Consider calling AddHs() .[04:49:38] Molecule does not have explicit Hs. Consider calling AddHs() ....................[04:50:17] WARNING: More than one matching pattern found - picking one [04:50:17] WARNING: More than one matching pattern found - picking one .[04:50:17] WARNING: More than one matching pattern found - picking one ... ---------------------------------------------------------------------- Ran 25 tests in 43.963s 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 0.231s OK .[04:50:24] Molecule does not have explicit Hs. Consider calling AddHs() F....[04:50:29] WARNING: not removing hydrogen atom without neighbors [04:50:29] WARNING: not removing hydrogen atom without neighbors [04:50:29] WARNING: not removing hydrogen atom without neighbors ....[04:50:29] WARNING: not removing hydrogen atom without neighbors ...... ====================================================================== FAIL: testGet3DMolDescriptors (__main__.TestCase.testGet3DMolDescriptors) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestDescriptors.py", line 216, in testGet3DMolDescriptors self.assertEqual(descs['PMI1'], 20.954531335493417) AssertionError: 20.954531335493083 != 20.954531335493417 ---------------------------------------------------------------------- Ran 16 tests in 5.185s FAILED (failures=1) [04:50:29] WARNING: Omitted undefined stereo [04:50:29] WARNING: Proton(s) added/removed ..[04:50:33] ERROR: Add/Remove protons error; *Conversion failed* [04:50:33] 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 3.744s FAILED (errors=1) InChI write Summary: 1160 identical, 0 suffix variance, 21 reasonable .... ---------------------------------------------------------------------- Ran 4 tests in 1.422s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.321s 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 0xffffae24f060>
\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 0xffffae24d9a0>NaN
1NaNrtzPeroxide<rdkit.Chem.rdchem.Mol object at 0xffffad6f22d0>yxcv
' ---------------------------------------------------------------------- Ran 28 tests in 2.361s FAILED (failures=2, skipped=2) ..............[04:50:51] WARNING: More than one matching pattern found - picking one [04:50:51] WARNING: More than one matching pattern found - picking one ..[04:50:51] Molecule does not have explicit Hs. Consider calling AddHs() [04:50:51] Molecule does not have explicit Hs. Consider calling AddHs() [04:50:51] Molecule does not have explicit Hs. Consider calling AddHs() [04:50:51] Molecule does not have explicit Hs. Consider calling AddHs() ......... ---------------------------------------------------------------------- Ran 25 tests in 10.746s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.111s OK ..s... ---------------------------------------------------------------------- Ran 6 tests in 2.025s OK (skipped=1) .. ---------------------------------------------------------------------- Ran 2 tests in 0.035s OK .............. ---------------------------------------------------------------------- Ran 14 tests in 8.707s OK ..[04:51:23] WARNING: not removing hydrogen atom without neighbors .[04:51:23] WARNING: not removing hydrogen atom without neighbors .[04:51:23] WARNING: no name column found on line 1 [04:51:23] WARNING: no name column found on line 2 [04:51:23] WARNING: no name column found on line 3 [04:51:23] WARNING: no name column found on line 4 [04:51:23] WARNING: no name column found on line 5 [04:51:23] WARNING: no name column found on line 6 [04:51:23] WARNING: no name column found on line 7 [04:51:23] WARNING: no name column found on line 8 [04:51:23] WARNING: no name column found on line 9 [04:51:23] WARNING: no name column found on line 10 [04:51:23] WARNING: no name column found on line 11 [04:51:23] WARNING: no name column found on line 12 [04:51:23] WARNING: no name column found on line 13 [04:51:23] WARNING: no name column found on line 14 [04:51:23] WARNING: no name column found on line 15 [04:51:23] WARNING: no name column found on line 16 [04:51:23] WARNING: no name column found on line 17 [04:51:23] WARNING: no name column found on line 18 [04:51:23] WARNING: no name column found on line 19 [04:51:23] WARNING: no name column found on line 20 [04:51:23] WARNING: no name column found on line 21 [04:51:23] WARNING: no name column found on line 22 [04:51:23] WARNING: no name column found on line 23 [04:51:23] WARNING: no name column found on line 24 [04:51:23] WARNING: no name column found on line 25 [04:51:23] WARNING: no name column found on line 26 [04:51:23] WARNING: no name column found on line 27 [04:51:23] WARNING: no name column found on line 28 [04:51:23] WARNING: no name column found on line 29 [04:51:23] WARNING: no name column found on line 30 [04:51:23] WARNING: no name column found on line 31 [04:51:23] WARNING: no name column found on line 32 [04:51:23] WARNING: no name column found on line 33 [04:51:23] WARNING: no name column found on line 34 [04:51:23] WARNING: no name column found on line 35 [04:51:23] WARNING: no name column found on line 36 [04:51:23] WARNING: no name column found on line 37 [04:51:23] WARNING: no name column found on line 38 [04:51:23] WARNING: no name column found on line 39 [04:51:23] WARNING: no name column found on line 40 [04:51:23] WARNING: no name column found on line 41 [04:51:23] WARNING: no name column found on line 42 [04:51:23] WARNING: no name column found on line 43 [04:51:23] WARNING: no name column found on line 44 [04:51:23] WARNING: no name column found on line 45 [04:51:23] WARNING: no name column found on line 46 [04:51:23] WARNING: no name column found on line 47 [04:51:23] WARNING: no name column found on line 48 [04:51:23] WARNING: no name column found on line 49 [04:51:23] WARNING: no name column found on line 50 [04:51:23] WARNING: no name column found on line 51 [04:51:23] WARNING: no name column found on line 52 [04:51:23] WARNING: no name column found on line 53 [04:51:23] WARNING: no name column found on line 54 [04:51:23] WARNING: no name column found on line 55 [04:51:23] WARNING: no name column found on line 56 [04:51:23] WARNING: no name column found on line 57 [04:51:23] WARNING: no name column found on line 58 [04:51:23] WARNING: no name column found on line 59 [04:51:23] WARNING: no name column found on line 60 [04:51:23] WARNING: no name column found on line 61 [04:51:23] WARNING: no name column found on line 62 [04:51:23] WARNING: no name column found on line 63 [04:51:23] WARNING: no name column 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[04:51:23] WARNING: no name column found on line 216 ...... ---------------------------------------------------------------------- Ran 10 tests in 0.149s OK .................. ---------------------------------------------------------------------- Ran 18 tests in 2.000s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.224s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.072s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.046s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.024s OK . ---------------------------------------------------------------------- Ran 1 test in 0.115s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.001s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.008s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.005s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.006s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.034s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.032s OK .... ---------------------------------------------------------------------- Ran 4 tests in 3.802s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.034s OK . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.003s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 0.050s OK .........[04:51:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. [04:51:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. [04:51:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. [04:51:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. .......[04:51:55] Molecule does not have explicit Hs. Consider calling AddHs() [04:51:55] Molecule does not have explicit Hs. Consider calling AddHs() ..... ---------------------------------------------------------------------- Ran 21 tests in 9.553s OK mol_197 219.68,35.94,110.98,11.56,110.32,11.04,95.23,10.25,0.00 mol_223 243.69,7.04,134.64,0.81,134.56,0.81,85.50,0.37,0.00 mol_269 216.59,3.99,105.00,0.87,103.81,0.89,89.27,0.92,6.00 . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK ...[04:51:57] **** 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 0.054s OK .. ---------------------------------------------------------------------- Ran 2 tests in 10.827s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.133s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.016s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.013s OK .....[04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors [04:52:12] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- Ran 10 tests in 0.467s OK ssssss..........s/build/reproducible-path/rdkit-202309.3/obj-aarch64-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 3.535s OK (skipped=7) sss. ---------------------------------------------------------------------- Ran 4 tests in 0.526s OK (skipped=3) ssss ---------------------------------------------------------------------- Ran 4 tests in 0.000s OK (skipped=4) .......... ---------------------------------------------------------------------- Ran 10 tests in 0.439s OK ...[04:52:20] SMARTS Parse Error: syntax error while parsing: boromicacid [04:52:20] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' [04:52:20] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide [04:52:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' [04:52:20] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride [04:52:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' [04:52:20] reaction has no reactants [04:52:20] reaction has no products [04:52:20] initialization failed [04:52:20] reaction has no reactants [04:52:20] reaction has no products . ---------------------------------------------------------------------- Ran 4 tests in 0.020s 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 0.007s OK ........................ ---------------------------------------------------------------------- Ran 24 tests in 0.047s OK !!! TEST FAILURE: python UnitTestDescriptors.py {} !!! TEST FAILURE: python UnitTestInchi.py {} !!! TEST FAILURE: python UnitTestPandasTools.py {} 6: [04:52:30] Finished: testMultipleTimes() 6: [04:52:30] 6: ----------------------------------------- 223/223 Test #6: testConcurrentQueue .................... Passed 246.94 sec 98% tests passed, 4 tests failed out of 223 Total Test time (real) = 247.06 sec The following tests FAILED: 1 - testInchi (Subprocess aborted) 21 - testConrec (Failed) 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-aarch64-linux-gnu' dh_auto_test: error: cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 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-aarch64-linux-gnu && make -j12 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-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-aarch64-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-aarch64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-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/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/spiral.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/retest.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/listutils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/fileutils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/comhack.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemutils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw_qax.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/cactvs.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/utils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/HTMLPiddler.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/testallps.ps -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__pycache__/pstests.cpython-312.pyc -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__pycache__/pidtest.cpython-312.pyc -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/testallps.py -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/pidSVG.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/pidReportLab.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/README -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt4.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/pidPyart.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/Fontmapping.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/psmetrics.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/fontinfo.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts -- Installing: 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/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/times-bold-12.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/times-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil -- Installing: 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/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/symbol-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.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/symbol-10.pil -- 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.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.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/courier-bold-10.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm -- 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-18.pbm -- 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/courier-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.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-10.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF -- Installing: 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/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 -- 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/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: 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/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/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: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMMPA.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMMPA.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMMPA.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRascalMCES.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRascalMCES.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRascalMCES.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalMCES.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalOptions.h -- Installing: /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 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so -- Installing: /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: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSLNParse.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSLNParse.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSLNParse.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNAttribs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParse.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParseOps.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdSLNParse.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdchem.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdmolops.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdqueries.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdmolfiles.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdtrajectory.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolStandardize.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/LinkNode.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitAbbreviations.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/GeneralizedSubstruct/XQMol.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/rdGeneralizedSubstruct.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/AndQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/LessQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/OrQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/Query.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/QueryObjects.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/RangeQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/SetQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Query/XOrQuery.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/Features/Feature.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /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-aarch64-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-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdCoordGen.so to rdCoordGen.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdDepictor.so to rdDepictor.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdDeprotect.so to rdDeprotect.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdDistGeom.so to rdDistGeom.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdFMCS.so to rdFMCS.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeneralizedSubstruct.so to rdGeneralizedSubstruct.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMMPA.so to rdMMPA.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolAlign.so to rdMolAlign.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolCatalog.so to rdMolCatalog.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolHash.so to rdMolHash.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolInterchange.so to rdMolInterchange.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolTransforms.so to rdMolTransforms.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdPartialCharges.so to rdPartialCharges.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdRascalMCES.so to rdRascalMCES.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdSLNParse.so to rdSLNParse.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdchem.so to rdchem.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdfragcatalog.so to rdfragcatalog.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdinchi.so to rdinchi.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdmolfiles.so to rdmolfiles.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdmolops.so to rdmolops.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdqueries.so to rdqueries.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdtrajectory.so to rdtrajectory.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-aarch64-linux-gnu.so I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-312-aarch64-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 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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: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package librdkit1t64: 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 librdkit-dev: 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: package librdkit1t64: 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 dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202309.3-7_arm64.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-7_arm64.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_arm64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-7_arm64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202309.3-7_all.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202309.3-7_arm64.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202309.3-7_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202309.3-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202309.3-7_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202309.3-7_arm64.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: user script /srv/workspace/pbuilder/871424/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/871424/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/871424 and its subdirectories I: Current time: Wed Nov 20 04:55:07 +14 2024 I: pbuilder-time-stamp: 1732028107